SMTL ID : 6q8n.1 (1 other biounit)

GH10 endo-xylanase in complex with xylobiose epoxide inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 6 residues within 4Å: Chain A: V.52, T.53, N.56, L.93, G.96, N.97 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.52 Hydrogen bonds: A:N.56, A:G.96, A:N.97 NAG.2: 3 residues within 4Å: Chain A: N.123, I.170, A.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.123, A:I.170 Water bridges: A:I.170

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

EDO.3: 1 residues within 4Å: Chain A: S.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.114 Water bridges: A:S.114 EDO.4: 7 residues within 4Å: Chain A: E.153, Y.196, Q.228, H.230, W.308 Ligands: EDO.6, HQ8.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.228 EDO.5: 2 residues within 4Å: Chain A: A.124, T.125 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: N.197, H.230, R.264 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.197, A:H.230, A:R.264, A:R.264 EDO.7: 3 residues within 4Å: Chain A: N.156, D.157, R.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.157, A:D.157 Water bridges: A:N.156, A:D.158 EDO.8: 1 residues within 4Å: Chain A: T.120 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.120 EDO.9: 7 residues within 4Å: Chain A: T.41, E.45, G.67, N.68, D.301, Y.306 Ligands: XYP.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.68, A:D.301, A:D.301 Water bridges: A:E.45 EDO.10: 4 residues within 4Å: Chain A: Q.79, G.119, T.120, W.121 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.79, A:T.120, A:T.120 Water bridges: A:Q.79 EDO.11: 5 residues within 4Å: Chain A: N.57, A.59, D.60, K.328, Y.332 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.57, A:K.328, A:Y.332 Water bridges: A:N.57 EDO.12: 3 residues within 4Å: Chain A: E.95, Q.99, K.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.99 Water bridges: A:E.95, A:L.101 EDO.13: 8 residues within 4Å: Chain A: K.71, W.72, T.105, L.106, W.108, N.110, Q.111, L.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.72, A:T.105, A:W.108, A:Q.111 EDO.14: 4 residues within 4Å: Chain A: W.308, S.311, T.312 Ligands: XYP.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.311, A:T.312 EDO.15: 7 residues within 4Å: Chain A: V.236, P.237, S.238, Q.276, S.279, D.280, A.283 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.237, A:Q.276 Water bridges: A:T.239, A:Q.276, A:A.283 EDO.16: 3 residues within 4Å: Chain A: Y.306, S.307, W.308 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.45

1 x K: POTASSIUM ION(Non-covalent)

K.17: 5 residues within 4Å: Chain A: L.34, C.288, V.289, T.291, C.294 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.288, A:T.291, A:C.294, H2O.1, H2O.9

1 x HQ8: (1~{R},2~{S},4~{S},5~{R})-cyclohexane-1,2,3,4,5-pentol(Covalent)

HQ8.18: 12 residues within 4Å: Chain A: K.71, H.104, W.108, N.152, E.153, Q.228, H.230, E.260, W.300, W.308 Ligands: EDO.4, XYP.19 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.260, A:W.308 Hydrogen bonds: A:K.71, A:K.71, A:H.104, A:N.152, A:E.153, A:Q.228

1 x XYP: beta-D-xylopyranose(Non-covalent)

XYP.19: 9 residues within 4Å: Chain A: N.68, K.71, W.108, Q.111, W.300, W.308 Ligands: EDO.9, EDO.14, HQ8.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.68, A:K.71, A:W.300 Water bridges: A:D.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schroder, S.P. et al., Dynamic and Functional Profiling of Xylan-Degrading Enzymes inAspergillusSecretomes Using Activity-Based Probes. Acs Cent.Sci. (2019)

Release Date

2019-06-05

Peptides

Beta-xylanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-xylanase

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