SMTL ID : 6ne9.1

Bacteroides intestinalis acetyl xylan esterase (BACINT_01039)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 7 residues within 4Å: Chain A: W.118, R.157, F.159, T.188, R.192 Chain B: I.110, R.192 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.157, B:R.192, B:R.192 Water bridges: A:W.118, A:E.144, A:E.144 PEG.2: 10 residues within 4Å: Chain A: L.142, G.191, R.192, K.195, N.197, L.198 Chain B: E.144, R.157 Ligands: EDO.5, EDO.18 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.195, A:N.197, B:E.144 PEG.3: 9 residues within 4Å: Chain A: Y.147, W.155, R.156, R.157, C.158, E.187, D.217, N.218, Y.220 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.147, A:R.156, A:R.157, A:R.157, A:N.218, A:N.218 PEG.12: 8 residues within 4Å: Chain B: S.233, I.234, F.235, E.236, E.237, Q.271, H.274, I.275 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.233, B:F.235, B:E.236, B:Q.271 PEG.13: 7 residues within 4Å: Chain B: T.298, H.334, P.335, F.336, P.337, G.338, K.341 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.338 PEG.14: 10 residues within 4Å: Chain A: E.144, R.157 Chain B: L.142, G.191, R.192, K.195, N.197, L.198 Ligands: EDO.9, PEG.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.195 PEG.15: 12 residues within 4Å: Chain B: E.33, V.34, F.92, I.110, F.112, E.123, R.192, Q.193, K.195, R.370 Ligands: EDO.9, PEG.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.33, B:E.123, B:K.195, B:R.370 PEG.16: 10 residues within 4Å: Chain A: L.141, Y.166, G.167, K.170, R.252 Chain B: Y.166, K.170, K.250, F.251, R.252 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.252, B:Y.166, B:R.252, B:R.252 Water bridges: A:G.167

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

EDO.4: 8 residues within 4Å: Chain A: S.233, I.234, F.235, E.236, E.237, Q.271, H.274, I.275 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.233, A:S.233, A:F.235, A:E.236, A:E.237, A:Q.271 EDO.5: 11 residues within 4Å: Chain A: E.33, V.34, F.92, I.110, F.112, E.123, R.192, Q.193, K.195, R.370 Ligands: PEG.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.33, A:E.123, A:R.192, A:K.195, A:R.370 EDO.6: 6 residues within 4Å: Chain A: D.128, F.131, Y.357, R.371, N.374, E.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.128, A:D.128, A:N.374, A:E.375 EDO.7: 8 residues within 4Å: Chain A: D.130, F.131, K.135, N.202, L.203, A.206, K.208, N.374 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.130, A:D.130, A:K.135 Water bridges: A:K.208, A:N.374 EDO.8: 5 residues within 4Å: Chain A: E.27, D.28, F.29, Q.43, R.51 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.27, A:F.29, A:R.51 Water bridges: A:Q.43, A:Q.43 EDO.9: 8 residues within 4Å: Chain A: E.144, N.146, R.157 Chain B: L.134, N.197, L.198 Ligands: PEG.14, PEG.15 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.146, B:N.197, B:N.197 Water bridges: A:N.146 EDO.10: 4 residues within 4Å: Chain A: R.48, P.87, Q.88, Q.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.48, A:R.48, A:Q.88 EDO.17: 7 residues within 4Å: Chain A: P.37 Chain B: Y.113, H.181, E.185, D.186, N.218, Y.220 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.218, B:N.218 Water bridges: B:E.187 EDO.18: 7 residues within 4Å: Chain A: L.134, N.197, L.198 Chain B: E.144, N.146, R.157 Ligands: PEG.2 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.144, B:N.146, B:R.157, A:N.197 EDO.19: 6 residues within 4Å: Chain B: D.128, F.131, Y.357, R.371, N.374, E.375 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.128, B:N.374, B:E.375, B:E.375 Water bridges: B:H.127, B:D.128 EDO.20: 7 residues within 4Å: Chain B: F.131, K.135, N.202, L.203, A.206, K.208, N.374 5 PLIP interactions: 5 interactions with chain B Water bridges: B:D.130, B:F.131, B:K.208, B:N.374, B:N.374 EDO.21: 9 residues within 4Å: Chain B: S.266, M.267, N.270, S.290, G.291, T.292, Y.295, F.336, H.364 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.266, B:S.266, B:N.270

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 5 residues within 4Å: Chain A: H.334, P.335, F.336, P.337, G.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.338 Salt bridges: A:H.334

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.22: 4 residues within 4Å: Chain A: I.110, R.192 Chain B: W.118, R.157 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pereira, G.V. et al., Degradation of complex arabinoxylans by human colonic Bacteroidetes. Nat Commun (2021)

Release Date

2019-12-25

Peptides

Isoamylase protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoamylase protein