Receptor
PDB id Resolution Class Description Source Keywords
5GLR 1.7 Å EC: 3.-.-.- CRYSTAL STRUCTURE OF COXYL43, GH43 BETA-XYLOSIDASE/ALPHA- ARABINOFURANOSIDASE FROM A COMPOSTMICROBIAL METAGENOME IN CW ITH L-ARABINOSE AND 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. 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
XYP XYP XYP B:404;
A:405;
Valid;
Valid;
none;
none;
submit data
414.36 n/a O(C1O...
NA B:402;
A:402;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
CA B:401;
A:401;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
FUB A:404;
B:403;
Valid;
Valid;
none;
Atoms found MORE than expected: % Diff = 1.3;
submit data
150.13 C5 H10 O5 C([C@...
ARA A:403;
Valid;
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. 2017
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 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 176 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 143 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 XYP XYP XYS 1 1
2 XYS XYS XYS XYS 1 1
3 XYS XYP XYP 1 1
4 XYP XYP XYP XYS 1 1
5 XYP XYP XYP XYP XYP 1 1
6 XYP XYP XYP XYP 1 1
7 XYP XYP XYP 1 1
8 XYP XYP XYP XYP XYP XYP 1 1
9 XYS XYS XYS XYS XYS 1 1
10 XYP XYS XYP 1 1
11 XYS XYS 0.904762 1
12 XYS XYP 0.904762 1
13 XYP XYS 0.904762 1
14 BXP 0.904762 1
15 XYP XYP 0.904762 1
16 XYS XYS XYS 0.791667 0.969697
17 XYS XYP AHR XYP 0.590909 0.888889
18 XYP XYP XYP AHR 0.590909 0.888889
19 XYP AHR XYP XYP 0.590909 0.888889
20 AHR XYP XYP XYP 0.575758 0.888889
21 AHR XYS XYP XYP XYP 0.560606 0.888889
22 XYP XYP GCV XYP 0.506494 0.888889
23 XYS XYS AZI 0.5 0.653061
24 XYP XYP TRS 0.5 0.744186
25 GCV XYP XYP XYS 0.493506 0.888889
26 XYP XYP XYP GCV 0.493506 0.888889
27 GCV XYP XYP XYP 0.493506 0.888889
28 AHR XYP XYP 0.484848 0.888889
29 AHR XYS XYS 0.484848 0.888889
30 XYP XYP AHR 0.484848 0.888889
31 XYS XYP AHR 0.484848 0.888889
32 XYS XYS NPO 0.455882 0.615385
33 XDN XYP 0.438596 0.756098
34 XYP XDN 0.438596 0.756098
35 XYP XIF 0.431034 0.704545
36 XIF XYP 0.431034 0.704545
37 GCV XYP XYP 0.415584 0.888889
38 GLC GLC XYP 0.405797 0.911765
Ligand no: 2; Ligand: FUB; Similar ligands found: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 Z6J 1 1
2 RIB 1 1
3 AHR 1 1
4 FUB 1 1
5 32O 1 1
6 MAN 0.653846 0.866667
7 BGC 0.653846 0.866667
8 GAL 0.653846 0.866667
9 ALL 0.653846 0.866667
10 WOO 0.653846 0.866667
11 GIV 0.653846 0.866667
12 BMA 0.653846 0.866667
13 GLA 0.653846 0.866667
14 GXL 0.653846 0.866667
15 GLC 0.653846 0.866667
16 FUB AHR 0.486486 0.875
17 AHR AHR 0.486486 0.875
18 GAF 0.483871 0.764706
19 GCS 0.483871 0.684211
20 G3F 0.483871 0.764706
21 PA1 0.483871 0.684211
22 SHG 0.483871 0.764706
23 G2F 0.483871 0.764706
24 1GN 0.483871 0.684211
25 2FG 0.483871 0.764706
26 X6X 0.483871 0.684211
27 2H5 0.483871 0.764706
28 3MG 0.46875 0.764706
29 SR1 0.466667 0.764706
30 2GS 0.454545 0.764706
31 AHR AHR AHR 0.45 0.875
32 FUB AHR AHR 0.45 0.875
33 RP5 0.441176 0.675
34 ABF 0.441176 0.675
35 HSX 0.441176 0.675
36 GAL BGC 0.439024 0.742857
37 MAL MAL 0.439024 0.722222
38 GAL GLC 0.439024 0.742857
39 CBK 0.439024 0.742857
40 MAL 0.439024 0.742857
41 N9S 0.439024 0.742857
42 BMA GAL 0.439024 0.742857
43 BGC GLC 0.439024 0.742857
44 GLA GAL 0.439024 0.742857
45 LAT 0.439024 0.742857
46 BGC BMA 0.439024 0.742857
47 BGC GAL 0.439024 0.742857
48 CBI 0.439024 0.742857
49 GLA GLA 0.439024 0.742857
50 LBT 0.439024 0.742857
51 GLC GAL 0.439024 0.742857
52 BMA BMA 0.439024 0.742857
53 MAB 0.439024 0.742857
54 GLC BGC 0.439024 0.742857
55 B2G 0.439024 0.742857
56 TRE 0.424242 0.742857
57 YIO 0.419355 0.757576
58 GLF 0.40625 0.735294
59 ALX 0.405405 0.619048
60 BNX 0.405405 0.619048
61 M3M 0.404762 0.742857
62 MAN GLC 0.404762 0.742857
63 LB2 0.404762 0.742857
64 GLA GAL GLC 0.4 0.742857
65 ASO 0.4 0.757576
66 MTT 0.4 0.742857
67 DXI 0.4 0.742857
68 CEX 0.4 0.742857
69 CE6 0.4 0.742857
70 MAN BMA BMA BMA BMA 0.4 0.742857
71 BGC BGC BGC BGC BGC BGC 0.4 0.742857
72 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.4 0.742857
73 BGC GLC GLC GLC GLC 0.4 0.742857
74 GLC GLC GLC GLC GLC GLC GLC 0.4 0.742857
75 GAL GAL GAL 0.4 0.742857
76 MAN MAN BMA BMA BMA BMA 0.4 0.742857
77 BMA BMA BMA BMA BMA 0.4 0.742857
78 B4G 0.4 0.742857
79 BGC GLC GLC GLC GLC GLC GLC 0.4 0.742857
80 GLC GAL GAL 0.4 0.742857
81 BMA MAN BMA 0.4 0.742857
82 BGC GLC GLC 0.4 0.742857
83 GLC BGC BGC BGC BGC BGC 0.4 0.742857
84 CTT 0.4 0.742857
85 GLC GLC BGC GLC GLC GLC GLC 0.4 0.742857
86 CT3 0.4 0.742857
87 GLC BGC BGC 0.4 0.742857
88 GLC GLC GLC GLC GLC GLC GLC GLC 0.4 0.742857
89 GLC BGC GLC 0.4 0.742857
90 CEY 0.4 0.742857
91 MLR 0.4 0.742857
92 BMA BMA MAN 0.4 0.722222
93 MAN BMA BMA 0.4 0.742857
94 GLC GLC GLC GLC GLC 0.4 0.742857
95 BGC GLC GLC GLC 0.4 0.742857
96 GLC GLC BGC 0.4 0.742857
97 BMA BMA BMA BMA BMA BMA 0.4 0.742857
98 CE5 0.4 0.742857
99 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.4 0.742857
100 CTR 0.4 0.742857
101 GLC BGC BGC BGC BGC 0.4 0.742857
102 BGC BGC BGC GLC 0.4 0.742857
103 BMA BMA BMA 0.4 0.742857
104 MT7 0.4 0.742857
105 CE8 0.4 0.742857
Ligand no: 3; Ligand: ARA; Similar ligands found: 14
No: Ligand ECFP6 Tc MDL keys Tc
1 XYP 1 1
2 0MK 1 1
3 RIP 1 1
4 LXC 1 1
5 ARA 1 1
6 ARB 1 1
7 XYS 1 1
8 HSY 1 1
9 BXP 0.414634 0.84375
10 XYP XYP 0.414634 0.84375
11 XYS XYP 0.414634 0.84375
12 XYS XYS 0.414634 0.84375
13 XYP XYS 0.414634 0.84375
14 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: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5GLN; Ligand: XYS; Similar sites found: 22
This union binding pocket(no: 2) in the query (biounit: 5gln.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3VSS FRU 0.00009351 0.40067 2.61628
2 1PT2 SUC 0.0003925 0.40422 3.48837
3 2CXG GLC GLC 0.03265 0.4023 4.36047
4 1W2T SUC GLA 0.0004179 0.40257 4.65116
5 1Y9G FRU 0.00003131 0.42056 4.94186
6 2X77 GDP 0.01593 0.40484 4.94186
7 3KF3 FRU 0.0003118 0.45335 5.81395
8 4N2R FUB 0.00002737 0.4221 6.28743
9 1G7C 5GP 0.01727 0.40695 6.38298
10 2CJW GDP 0.01107 0.41652 6.77083
11 3PIJ FRU 0.0001943 0.40238 6.84411
12 2OBM ADP 0.00242 0.46436 6.97674
13 2YFT DQR 0.0005393 0.41282 8.13953
14 3AKI AH8 0.00006978 0.43808 9.01163
15 5JOX EDG 0.0000003297 0.64919 10.4651
16 1YRX FMN 0.01003 0.40702 13.2231
17 3D5Z FUB AHR AHR 0.001037 0.41258 13.3758
18 3WN0 FUB 0.0004147 0.43078 14.1553
19 2GUC MAN 0.006194 0.43611 14.7541
20 2NU5 NAG 0.006664 0.4346 14.7541
21 2NUO BGC 0.02121 0.40209 14.7541
22 2EXK XYS XYS 0.00000687 0.47099 21.8023
Pocket No.: 3; Query (leader) PDB : 5GLN; Ligand: XYP XYP XYP; Similar sites found: 17
This union binding pocket(no: 3) in the query (biounit: 5gln.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WCX MET 0.03223 0.40222 1.16279
2 4CJN QNZ 0.008925 0.44043 1.74419
3 5AMC GLY NIY 0.02539 0.40667 2.32558
4 1B09 PC 0.02281 0.40765 2.91262
5 5JCM NAD 0.02369 0.40059 3.54767
6 3MAN BMA BMA MAN 0.04266 0.40308 3.64238
7 5MUL BDP 0.01866 0.42031 4.36047
8 1Y9G FRU 0.0000374 0.40016 4.94186
9 3KF3 FRU 0.0001692 0.45002 5.81395
10 4N2R FUB 0.00003282 0.40152 6.28743
11 2OBM ADP 0.006075 0.44644 6.97674
12 3AKI AH8 0.00009088 0.41662 9.01163
13 5JOX EDG 0.0000004225 0.65105 10.4651
14 2ZFZ ARG 0.04423 0.40235 11.3924
15 3WN0 FUB 0.0002824 0.41997 14.1553
16 2NUO BGC 0.02436 0.40237 14.7541
17 2EXK XYS XYS 0.00001013 0.44438 21.8023
Pocket No.: 4; Query (leader) PDB : 5GLN; Ligand: XYS; Similar sites found: 8
This union binding pocket(no: 4) in the query (biounit: 5gln.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WCX MET 0.03223 0.40222 1.16279
2 4CJN QNZ 0.008925 0.44043 1.74419
3 5AMC GLY NIY 0.02539 0.40667 2.32558
4 1B09 PC 0.02281 0.40765 2.91262
5 5JCM NAD 0.02369 0.40059 3.54767
6 3MAN BMA BMA MAN 0.04266 0.40308 3.64238
7 5MUL BDP 0.01866 0.42031 4.36047
8 2ZFZ ARG 0.04423 0.40235 11.3924
Pocket No.: 5; Query (leader) PDB : 5GLN; Ligand: XYP XYP XYP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5gln.bio2) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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