-->
Receptor
PDB id Resolution Class Description Source Keywords
5GLN 1.7 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF COXYL43, GH43 BETA-XYLOSIDASE/ALPHA- ARABINOFURANOSIDASE FROM A COMPOSTMICROBIAL METAGENOME IN CW ITH XYLOTRIOSE, CALCIUM-BOUND FORM UNCULTURED BACTERIUM GLYCOSIDE HYDROLASE FAMILY 43 HYDROLASE
Ref.: CRYSTAL STRUCTURE OF METAGENOMIC BETA-XYLOSIDASE/ ALPHA-L-ARABINOFURANOSIDASE ACTIVATED BY CALCIUM. J. BIOCHEM. V. 162 173 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT B:611;
A:613;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
CA B:401;
A:401;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
XYP XYP XYP B:511;
B:501;
Valid;
Valid;
none;
none;
submit data
414.36 n/a O(C1C...
XYP A:532;
Valid;
none;
submit data
150.13 C5 H10 O5 C1[C@...
NA B:411;
A:411;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
XYP XYP A:511;
A:501;
Valid;
Valid;
none;
none;
submit data
164.157 n/a O(C)C...
XYS B:500;
A:500;
Valid;
Valid;
none;
none;
submit data
150.13 C5 H10 O5 C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5GLN 1.7 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF COXYL43, GH43 BETA-XYLOSIDASE/ALPHA- ARABINOFURANOSIDASE FROM A COMPOSTMICROBIAL METAGENOME IN CW ITH XYLOTRIOSE, CALCIUM-BOUND FORM UNCULTURED BACTERIUM GLYCOSIDE HYDROLASE FAMILY 43 HYDROLASE
Ref.: CRYSTAL STRUCTURE OF METAGENOMIC BETA-XYLOSIDASE/ ALPHA-L-ARABINOFURANOSIDASE ACTIVATED BY CALCIUM. J. BIOCHEM. V. 162 173 2017
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 253 families.
1 5GLM - XYP XYP n/a n/a
2 5GLP - ARA C5 H10 O5 C1[C@@H]([....
3 5GLR - FUB C5 H10 O5 C([C@H]1[C....
4 5GLQ - FUB C5 H10 O5 C([C@H]1[C....
5 5GLN - XYP XYP XYP n/a n/a
6 5GLO - ARA C5 H10 O5 C1[C@@H]([....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 5GLM - XYP XYP n/a n/a
2 5GLP - ARA C5 H10 O5 C1[C@@H]([....
3 5GLR - FUB C5 H10 O5 C([C@H]1[C....
4 5GLQ - FUB C5 H10 O5 C([C@H]1[C....
5 5GLN - XYP XYP XYP n/a n/a
6 5GLO - ARA C5 H10 O5 C1[C@@H]([....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 173 families.
1 5GLM - XYP XYP n/a n/a
2 5GLP - ARA C5 H10 O5 C1[C@@H]([....
3 5GLR - FUB C5 H10 O5 C([C@H]1[C....
4 5GLQ - FUB C5 H10 O5 C([C@H]1[C....
5 5GLN - XYP XYP XYP n/a n/a
6 5GLO - ARA C5 H10 O5 C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: XYP XYP XYP; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 XYS XYS XYS XYS 1 1
2 XYP XYP XYP XYP 1 1
3 XYP XYP XYS 1 1
4 XYS XYS XYS XYS XYS 1 1
5 XYP XYP XYP XYP XYP XYP 1 1
6 XYP XYP XYP XYP XYP XYP XYP 1 1
7 XYS XYP XYP 1 1
8 XYP XYP XYP 1 1
9 XYP XYP XYP XYS 1 1
10 XYP XYS XYP 1 1
11 XYP XYP XYP XYP XYP 1 1
12 BXP 0.904762 1
13 XYS XYP 0.904762 1
14 XYP XYS 0.904762 1
15 XYS XYS XYS 0.791667 0.969697
16 XYP XYP XYP AHR 0.590909 0.888889
17 XYS XYP AHR XYP 0.590909 0.888889
18 XYP AHR XYP XYP 0.590909 0.888889
19 AHR XYP XYP XYP 0.575758 0.888889
20 AHR XYS XYP XYP XYP 0.560606 0.888889
21 XYS XYS 0.511111 0.939394
22 XYP XYP TRS 0.508197 0.711111
23 XYP XYP GCV XYP 0.506494 0.888889
24 XYS XYS AZI 0.5 0.653061
25 XYP XYP XYP GCV 0.493506 0.888889
26 GCV XYP XYP XYS 0.493506 0.888889
27 GCV XYP XYP XYP 0.493506 0.888889
28 AHR XYP XYP 0.484848 0.888889
29 XYP XYP AHR 0.484848 0.888889
30 XYS XYP AHR 0.484848 0.888889
31 AHR XYS XYS 0.484848 0.888889
32 XYS XYS NPO 0.455882 0.615385
33 XYP XDN 0.438596 0.704545
34 XIF XYP 0.438596 0.659574
35 XYP XIF 0.438596 0.659574
36 XDN XYP 0.438596 0.704545
37 GCV XYP XYP 0.415584 0.888889
38 GLC GLC XYP 0.405797 0.911765
Ligand no: 2; Ligand: XYP; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 RIP 1 1
2 XYS 1 1
3 ARB 1 1
4 HSY 1 1
5 ARA 1 1
6 XYP 1 1
7 LXC 1 1
8 0MK 1 1
9 XYP XYS 0.414634 0.84375
10 BXP 0.414634 0.84375
11 XYS XYP 0.414634 0.84375
12 FU4 0.4 0.896552
Ligand no: 3; Ligand: XYP XYP; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 ARW 1 1
2 XYP XYP 1 1
3 X1P 0.461538 0.651163
4 XS2 0.44 0.842105
5 XLM 0.431373 0.837838
6 XYP XYS 0.422222 0.828571
7 XYS XYP 0.422222 0.828571
8 BXP 0.422222 0.828571
Ligand no: 4; Ligand: XYS; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 RIP 1 1
2 XYS 1 1
3 ARB 1 1
4 HSY 1 1
5 ARA 1 1
6 XYP 1 1
7 LXC 1 1
8 0MK 1 1
9 XYP XYS 0.414634 0.84375
10 BXP 0.414634 0.84375
11 XYS XYP 0.414634 0.84375
12 FU4 0.4 0.896552
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5GLN; Ligand: XYP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5gln.bio1) has 4 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5GLN; Ligand: XYS; Similar sites found with APoc: 84
This union binding pocket(no: 2) in the query (biounit: 5gln.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 4IHQ ADP 1.45349
3 4GN8 ASO 1.67224
4 5FMD NYT 1.74419
5 3BJE URA 1.74419
6 5U75 SIA GAL NDG FUC 1.78571
7 3WCZ CIT 1.94805
8 4M3P HCS 2.03488
9 2EAE FUL 2.03488
10 2PEL LAT 2.11864
11 2PEL LBT 2.11864
12 1NXJ GLV 2.18579
13 3VSS FRU 2.61628
14 3TBK ANP 2.88288
15 2VK2 GZL 2.94118
16 1LW4 TLP 3.19767
17 2Y7P SAL 3.21101
18 3SHR CMP 3.34448
19 3I9U DTU 3.42205
20 1PT2 SUC 3.48837
21 2HJR CIT 3.65854
22 2ILZ GTP 3.77907
23 1BCJ NGA 3.8961
24 6F1J EDG 4
25 4NOS ITU 4.06977
26 5XHA FRU FRU 4.06977
27 2CXG GLC GLC 4.36047
28 3PQC GDP 4.61538
29 1W2T SUC GLA 4.65116
30 1Y9G FRU 4.94186
31 2X77 GDP 4.94186
32 3EZ2 ADP 4.94186
33 5A96 GTP 5.22088
34 6EW3 S3C 5.60345
35 3KF3 FRU 5.81395
36 2BKL ZAH 5.81395
37 2O0J ADP 6.10465
38 4XZ9 G3P 6.27803
39 4N2R FUB 6.28743
40 4N2R AHR 6.28743
41 1G7C 5GP 6.38298
42 2WJH GDP 6.62651
43 2ADD SUC 6.68605
44 2CJW GDP 6.77083
45 3PIJ FRU 6.84411
46 2OBM ADP 6.97674
47 1RVV INI 7.14286
48 3CF6 SP1 7.18563
49 3KIH GDL 7.2165
50 1VKJ A3P 7.36842
51 4DCT GDP 7.55814
52 2YFT DQR 8.13953
53 3WFD AXO 8.21918
54 1H8P PC 8.25688
55 1UI0 URA 8.78049
56 3AKI AH8 9.01163
57 1RE0 GDP 9.50226
58 4RYV ZEA 9.67742
59 2CHN NGT 9.88372
60 6A9F 9BF 10.3139
61 5JOX EDG 10.4651
62 1F6B GDP 10.6061
63 1GXU 2HP 10.989
64 3AB4 THR 11.236
65 5AYE BMA BMA 12.8358
66 6A8H AHR AHR AHR 13.0841
67 1YRX FMN 13.2231
68 5ZQS BXP 13.3721
69 3WN0 FUB 14.1553
70 2GUD MAN 14.7541
71 2GUC MAN 14.7541
72 2NU5 NAG 14.7541
73 2HYQ MAN MAN 14.7541
74 2HYR BGC GLC 14.7541
75 2NUO BGC 14.7541
76 6FLZ MMA 15.9722
77 3O94 NCA 17.5355
78 2EXK XYS XYS 21.8023
79 5Z5I FUB 26.1628
80 5Z5I XYS 26.1628
81 5Z5I XYP 26.1628
82 6AZQ C5J 28.2443
83 6EIZ FOH 34.375
84 3C7F XYP XYP XYP 47.093
Pocket No.: 3; Query (leader) PDB : 5GLN; Ligand: XYP XYP XYP; Similar sites found with APoc: 94
This union binding pocket(no: 3) in the query (biounit: 5gln.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 6CS9 PIO None
2 4WG0 CHD None
3 4WCX MET 1.16279
4 4IHQ ADP 1.45349
5 4GN8 ASO 1.67224
6 5FMD NYT 1.74419
7 4CJN QNZ 1.74419
8 3BJE URA 1.74419
9 2EAE FUL 2.03488
10 2PEL LAT 2.11864
11 2PEL LBT 2.11864
12 1NXJ GLV 2.18579
13 4EZD SEY 2.32558
14 5AMC GLY NIY 2.32558
15 3VSS FRU 2.61628
16 5M1Z 6LW AHR 2.61628
17 3TBK ANP 2.88288
18 1B09 PC 2.91262
19 3OUM TOF 3.01724
20 3ITA AIC 3.19767
21 1LW4 TLP 3.19767
22 2IBN I1N 3.2
23 3SHR CMP 3.34448
24 1PT2 SUC 3.48837
25 1F9V ADP 3.48837
26 5JCM NAD 3.54767
27 3MAN BMA BMA MAN 3.64238
28 2HJR CIT 3.65854
29 1MZC SUC 3.77907
30 1LDN OXM 3.79747
31 1BCJ NGA 3.8961
32 3SQG COM 3.94265
33 6F1J EDG 4
34 5XHA FRU FRU 4.06977
35 4NOS ITU 4.06977
36 5MUL BDP 4.36047
37 3A72 AHR AHR 4.36047
38 3PQC GDP 4.61538
39 1W2T SUC GLA 4.65116
40 1Y9G FRU 4.94186
41 5A96 GTP 5.22088
42 6EW3 S3C 5.60345
43 5CK5 GDP 5.6962
44 3KF3 FRU 5.81395
45 2HK9 ATR 5.81818
46 2O0J ADP 6.10465
47 4XZ9 G3P 6.27803
48 4N2R FUB 6.28743
49 4N2R AHR 6.28743
50 2ADD SUC 6.68605
51 3PIJ FRU 6.84411
52 3ZDS OMD 6.92841
53 2OBM ADP 6.97674
54 3QMN A3P 6.97674
55 4DCT GDP 7.55814
56 2YFT DQR 8.13953
57 1KW6 BPY 8.21918
58 3WFD AXO 8.21918
59 1H8P PC 8.25688
60 3KP6 SAL 8.60927
61 1LNX URI 8.64198
62 1UI0 URA 8.78049
63 3AKI AH8 9.01163
64 3LIH RAF 9.30233
65 1YZG GDP 9.49721
66 3H0L ADP 9.57447
67 2J73 GLC GLC GLC GLC 9.70874
68 2CHN NGT 9.88372
69 5JOX EDG 10.4651
70 1F6B GDP 10.6061
71 2ZFZ ARG 11.3924
72 5AYE BMA BMA 12.8358
73 6A8H AHR AHR AHR 13.0841
74 1X0P FAD 13.2867
75 5ZQS BXP 13.3721
76 3WN0 FUB 14.1553
77 2HYR BGC GLC 14.7541
78 2NU5 NAG 14.7541
79 2GUD MAN 14.7541
80 2GUD BMA 14.7541
81 2GUC MAN 14.7541
82 2NUO BGC 14.7541
83 2BMR 3NT 15.4639
84 6FLZ MMA 15.9722
85 1BO4 COA 16.0714
86 1VBO MAN 17.4497
87 3O94 NCA 17.5355
88 2EXK XYS XYS 21.8023
89 5Z5I FUB 26.1628
90 5Z5I XYS 26.1628
91 5Z5I XYP 26.1628
92 5C2N NAG 27.0833
93 6AZQ C5J 28.2443
94 3C7F XYP XYP XYP 47.093
Pocket No.: 4; Query (leader) PDB : 5GLN; Ligand: XYS; Similar sites found with APoc: 36
This union binding pocket(no: 4) in the query (biounit: 5gln.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 6CS9 PIO None
2 4WCX MET 1.16279
3 4CJN QNZ 1.74419
4 4EZD SEY 2.32558
5 5AMC GLY NIY 2.32558
6 5M1Z 6LW AHR 2.61628
7 1B09 PC 2.91262
8 3OUM TOF 3.01724
9 3ITA AIC 3.19767
10 2IBN I1N 3.2
11 1F9V ADP 3.48837
12 5JCM NAD 3.54767
13 3MAN BMA BMA MAN 3.64238
14 1MZC SUC 3.77907
15 1LDN OXM 3.79747
16 3SQG COM 3.94265
17 5MUL BDP 4.36047
18 3A72 AHR AHR 4.36047
19 5CK5 GDP 5.6962
20 2HK9 ATR 5.81818
21 3ZDS OMD 6.92841
22 3QMN A3P 6.97674
23 1KW6 BPY 8.21918
24 3KP6 SAL 8.60927
25 1LNX URI 8.64198
26 3LIH RAF 9.30233
27 1YZG GDP 9.49721
28 3H0L ADP 9.57447
29 2J73 GLC GLC GLC GLC 9.70874
30 2ZFZ ARG 11.3924
31 1X0P FAD 13.2867
32 2GUD BMA 14.7541
33 2BMR 3NT 15.4639
34 1BO4 COA 16.0714
35 1VBO MAN 17.4497
36 5C2N NAG 27.0833
Pocket No.: 5; Query (leader) PDB : 5GLN; Ligand: XYP XYP XYP; Similar sites found with APoc: 191
This union binding pocket(no: 5) in the query (biounit: 5gln.bio2) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 4XCZ FON 1.45349
2 4XCZ T3Q 1.45349
3 1QPG MAP 1.45349
4 4LXQ FON 1.45985
5 4LXQ TYD 1.45985
6 6MB9 NMY 1.45985
7 6MB9 COA 1.45985
8 2R42 FPS 1.74419
9 1OYY AGS 1.74419
10 1X8J A3P 1.74419
11 6GD6 EVB 1.85185
12 3GBR PRP 2.02899
13 5UIJ TYD 2.03488
14 2ZB4 NAP 2.03488
15 2ZB4 5OP 2.03488
16 5MW4 5JU 2.09581
17 5EYG NAP 2.26415
18 1KGZ PRP 2.32558
19 1SKQ GDP 2.32558
20 1ZCB GDP 2.32558
21 2X7J TPP 2.32558
22 4AX7 4MU BGC BGC 2.32558
23 2E9L PLM 2.32558
24 3WCS MAN NAG GAL 2.3622
25 2FZH DH1 2.42718
26 3O3R NAP 2.53165
27 3NGL NAP 2.53623
28 1YRE COA 2.53807
29 4UCF GLA 2.61628
30 4RGA 3PV 2.61628
31 4M0R 644 2.61628
32 4IV9 FAD 2.61628
33 3FHR P4O 2.67857
34 6GCB GSH 2.76923
35 1ZUA NAP 2.83912
36 1ZUA TOL 2.83912
37 5FJJ MAN 2.90698
38 5LB3 ADP 2.90698
39 2E22 MAN 2.90698
40 3VET TOY 2.90698
41 2B4R NAD 2.90698
42 2B4R AES 2.90698
43 1RF6 GPJ 2.90698
44 1RF6 S3P 2.90698
45 6CHP F0Y 3.10559
46 5H62 UDP 3.16092
47 2AKO ADP 3.18725
48 2FSH ANP 3.19767
49 2C1X UDP 3.19767
50 3ZJ0 ACO 3.39806
51 3H4V DVP 3.47222
52 3H4V NAP 3.47222
53 1QPB PYM 3.48837
54 1QPB TPP 3.48837
55 1MO9 KPC 3.48837
56 1MO9 FAD 3.48837
57 4H03 NAD 3.48837
58 3MAX LLX 3.48837
59 5XET ME8 3.48837
60 3NRR D16 3.48837
61 4ITM ATP 3.49206
62 2Q7V FAD 3.69231
63 4TMK T5A 3.75587
64 2D4V NAD 3.77907
65 1HEX NAD 3.77907
66 1JQN DCO 3.77907
67 3HWW AKG 3.77907
68 2ZEJ GDP 3.80435
69 1J3I NDP 3.96341
70 6GBC AMP 4.06977
71 4EDF UPG 4.06977
72 4B3J COA 4.06977
73 1C3V NDP 4.08163
74 3V2U ATP 4.10959
75 6EDK 1YA 4.14747
76 2JE7 XMM 4.1841
77 2BL9 CP6 4.20168
78 2BL9 NDP 4.20168
79 5VYR B62 4.21456
80 5VYR GMP 4.21456
81 1U72 NDP 4.30108
82 1U72 MTX 4.30108
83 2NUN ADP 4.33437
84 4U31 MVP 4.36047
85 6FFL GLC GLC GLC 4.36047
86 2FWP ICR 4.37158
87 2II3 CAO 4.58015
88 2VZZ SCA 4.58716
89 4LIK CIT 4.65116
90 1GTE FAD 4.65116
91 1UCD U5P 4.73684
92 1UCD URA 4.73684
93 5FIT AP2 4.7619
94 1O3Y GTP 4.81928
95 3DKP ADP 4.89796
96 3CX8 GSP 4.92611
97 1EM6 CP4 4.94186
98 2PID YSA 4.94186
99 3HBF MYC 4.94186
100 3HBF UDP 4.94186
101 2CIG 1DG 5.03145
102 5OYH T99 5.18135
103 1AOE GW3 5.20833
104 1AOE NDP 5.20833
105 2D3N GLC GLC GLC 5.23256
106 2D3N GLC GLC 5.23256
107 2C42 PYR 5.23256
108 2C42 TPP 5.23256
109 1G16 GDP 5.29412
110 3W9F I3P 5.38462
111 1ZRH A3P 5.47445
112 4YS0 ADP 5.52326
113 5H68 AGS 5.58824
114 2AMV BIN 5.81395
115 2WN6 NDP 5.81395
116 5MIT NAP 5.81395
117 5MIT FAD 5.81395
118 1IIM TTP 5.82192
119 5YVT NAI 5.8997
120 4D42 W0I 6.02837
121 4D42 NAP 6.02837
122 3AHC TPP 6.10465
123 3NUB UD0 6.10465
124 3CIF NAD 6.10465
125 4J36 FAD 6.10465
126 4TM3 FAD 6.10465
127 4NTO 1PW 6.28019
128 3KJS DQ1 6.39535
129 2IW3 ADP 6.39535
130 3KJS NAP 6.39535
131 5YQW CBS 6.39535
132 3G6K FAD 6.49351
133 3G6K POP 6.49351
134 4NP3 2L2 6.66667
135 2VBF TPP 6.68605
136 5GQX GLC GLC GLC GLC GLC GLC GLC 6.68605
137 3IX9 NDP 6.84211
138 2VK4 TPP 6.97674
139 2Q6B HR2 6.97674
140 4HCX NDP 6.97674
141 3GRU AMP 7.11864
142 4EIP FAD 7.26744
143 4I4B NAD 7.26744
144 5EXE 5SR 7.26744
145 5OCQ CIT 7.36842
146 1VKJ A3P 7.36842
147 1U70 MTX 7.52688
148 1U70 NDP 7.52688
149 4R57 ACO 7.95455
150 2CNT COA 8.125
151 3D2M COA 8.13953
152 5AM1 I5T 8.13953
153 3BD9 A3P 8.21429
154 5FQD LVY 8.5044
155 3Q9N COA 8.86076
156 6C0B MLI 9.01163
157 4YFY 1YJ 9.05512
158 1KQN NAD 9.319
159 4OOE NDP 9.59302
160 4UOZ GLA 9.59302
161 6C90 ADP 9.61539
162 4XPL ACO 9.81595
163 1ZPD DPX 9.88372
164 3HVJ 705 9.95475
165 3CYI ATP 10
166 3HY2 ATP 10
167 3ITJ FAD 10.0592
168 4XUC SAM 10.0917
169 4XUC 43G 10.0917
170 4KVX ACO 10.2564
171 4OAS 2SW 10.4167
172 1VPE ANP 10.4651
173 1XEX ATP 10.4651
174 3ZFD ANP 10.4651
175 3EEL 53T 10.5727
176 1IG3 VIB 10.6464
177 3B7G ANP 10.8696
178 3WR7 COA 11.1765
179 1OT6 HC4 11.2
180 1OZH HE3 12.2093
181 2BW7 ECS 12.7854
182 2BW7 APC 12.7854
183 3AKK ADP 13.5385
184 1VBH PEP 13.9535
185 2MJP ANP 14.5078
186 5HW4 SAM 14.9194
187 1RC0 KT5 16.7464
188 2D7D ADP 20
189 5Z84 PGV 20.339
190 2DYS PGV 20.339
191 5ZCO PGV 20.339
APoc FAQ
Feedback