SMTL ID : 5msx.1

Glycoside hydrolase BT_3662

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 6 residues within 4Å: Chain A: S.147, N.149, G.151, R.171, H.173, V.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.147, A:N.149, A:R.171

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 1 residues within 4Å: Chain A: H.260 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.260, H2O.1, H2O.2, H2O.3, H2O.3 CA.3: 6 residues within 4Å: Chain A: F.357, D.360, A.362, S.365, W.454, E.455 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:F.357, A:A.362, A:S.365, A:S.365, A:W.454 CA.6: 1 residues within 4Å: Chain B: H.260 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.260, H2O.6, H2O.6, H2O.7, H2O.8 CA.7: 6 residues within 4Å: Chain B: F.357, D.360, A.362, S.365, W.454, E.455 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:F.357, B:D.360, B:A.362, B:S.365, B:S.365 CA.16: 1 residues within 4Å: Chain C: H.260 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:H.260, H2O.12, H2O.13, H2O.14, H2O.14 CA.17: 6 residues within 4Å: Chain C: F.357, D.360, A.362, S.365, W.454, E.455 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:F.357, C:A.362, C:S.365, C:S.365, C:W.454

22 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: T.269, D.270, N.271 Chain C: I.42, N.43, F.99, Y.104 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain B: D.36, W.92, E.200, R.286 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain B: G.56, Q.57, G.58, S.283, T.284, N.285 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: T.61, S.62, K.88, E.89, K.90 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: G.112, Y.113, G.151, G.152 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain B: K.103, Y.105, A.129, D.180 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain B: F.139, T.140, P.141, T.143, L.145, Q.146, S.147, K.148 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: K.208, D.270, Y.272 Chain C: R.130, G.131 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: Q.292, L.293, K.294, R.302, P.303, V.304, E.305 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain C: D.36, L.59, W.92, R.286 Ligands: EDO.25 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain C: Q.40, E.41, K.96, F.264, H.265 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain C: G.56, Q.57, G.58, S.283, T.284, N.285 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: K.316 Chain C: F.158, V.159, D.160, D.161, K.206 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain C: L.145, Q.146, S.147, V.184, D.185 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain C: S.192, T.193, P.194, F.238 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain C: R.195, E.242, Q.243, D.244, I.245 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain C: D.36, A.93, I.153, D.154, E.200 Ligands: EDO.18 Ligand excluded by PLIP EDO.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain C: Q.292, L.293, K.294, R.302, P.303, V.304, E.305 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain C: P.266, N.271, Y.273, L.314 Ligand excluded by PLIP EDO.29: 10 residues within 4Å: Chain C: I.394, Y.395, F.396, P.399, G.402, H.403, K.426, C.428, S.429, H.431 Ligand excluded by PLIP EDO.30: 1 residues within 4Å: Chain C: R.425 Ligand excluded by PLIP

1 x 144: TRIS-HYDROXYMETHYL-METHYL-AMMONIUM(Non-covalent)

144.5: 7 residues within 4Å: Chain A: D.36, W.92, I.153, D.154, E.200, H.260, R.286 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.200, A:Y.223, A:H.260, A:R.286, A:R.286 Salt bridges: A:D.36, A:D.154, A:E.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ndeh, D. et al., Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Nature (2017)

Release Date

2017-03-22

Peptides

Putative endo-1,4-beta-xylanase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Putative endo-1,4-beta-xylanase