SMTL ID : 3vsv.1

The complex structure of XylC with xylose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-tetramer

Ligands

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

XYP.1: 13 residues within 4Å: Chain A: W.113, P.233, Q.289, H.352, E.353, K.358, H.360, W.380, D.382, W.383, E.405, V.406, R.450 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.289, A:K.358, A:H.360, A:W.383, A:E.405, A:E.405, A:R.450 Salt bridges: A:H.352, A:K.358 XYP.2: 6 residues within 4Å: Chain A: K.163, H.339, Y.341, R.371, H.373, D.559 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.163, A:K.163, A:H.373 Water bridges: A:Y.341, A:H.373 XYP.3: 6 residues within 4Å: Chain A: T.584, K.585, E.604 Chain C: D.57, K.58 Ligands: XYP.20 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:T.584, A:K.585, C:D.57, C:D.57 Water bridges: A:K.603, A:E.604, A:E.604, C:D.57, C:K.58 Salt bridges: A:K.585 XYP.4: 5 residues within 4Å: Chain A: D.57, I.250, I.310, R.312 Ligands: XYS.25 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.57, A:D.57, A:R.312, A:R.312 Water bridges: A:D.57, A:R.60 XYP.5: 7 residues within 4Å: Chain A: Y.134, V.136, P.145, Q.146, R.148, T.168, V.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.146, A:Q.146, A:T.168 Salt bridges: A:R.148 XYP.6: 7 residues within 4Å: Chain A: Q.366, H.368, H.369, R.389, S.391, K.392, D.613 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.366, A:S.391, A:S.391, A:K.392, A:D.613 Water bridges: A:Q.366, A:T.609 Salt bridges: A:H.368, A:H.369, A:K.392 XYP.7: 6 residues within 4Å: Chain A: T.211, W.245, E.269, N.299 Chain B: T.211, N.299 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.211, B:N.299, B:N.299, A:T.211, A:N.299 Water bridges: B:T.211, B:T.211, B:E.269, A:T.211, A:T.271 XYP.10: 13 residues within 4Å: Chain B: W.113, P.233, Q.289, H.352, E.353, K.358, H.360, W.380, D.382, W.383, E.405, V.406, R.450 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.289, B:K.358, B:H.360, B:W.383, B:E.405, B:E.405, B:R.450 Salt bridges: B:H.352, B:K.358 XYP.11: 5 residues within 4Å: Chain B: H.339, Y.341, R.371, H.373, D.559 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.373 Water bridges: B:K.163, B:K.163, B:N.342, B:N.342, B:R.371, B:H.373, B:D.374 XYP.12: 6 residues within 4Å: Chain B: T.584, K.585, E.604 Chain D: D.57, K.58 Ligands: XYP.30 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Water bridges: B:E.604 Salt bridges: B:K.585 Hydrogen bonds: D:D.57 XYP.13: 7 residues within 4Å: Chain B: D.57, I.250, I.310, R.312, Y.336 Chain D: K.603 Ligands: XYP.29 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.57 Water bridges: B:D.57, B:R.60 Salt bridges: B:R.312 XYP.14: 6 residues within 4Å: Chain B: Q.366, H.368, H.369, R.389, S.391, K.392 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Q.366, B:S.391, B:S.391, B:K.392 Water bridges: B:R.389, B:R.389, B:K.392, B:K.392 Salt bridges: B:H.368, B:H.369, B:K.392 XYP.15: 7 residues within 4Å: Chain B: Y.134, V.136, P.145, Q.146, R.148, T.168, V.171 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.146, B:Q.146, B:R.148, B:R.148 XYP.18: 13 residues within 4Å: Chain C: W.113, P.233, Q.289, H.352, E.353, K.358, H.360, W.380, D.382, W.383, E.405, V.406, R.450 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.289, C:K.358, C:H.360, C:W.383, C:E.405, C:E.405, C:R.450 Salt bridges: C:H.352, C:K.358 XYP.19: 5 residues within 4Å: Chain C: K.163, H.339, Y.341, R.371, H.373 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.163, C:K.163, C:H.373, C:D.559 Water bridges: C:Y.341, C:R.371, C:R.371 Salt bridges: C:H.339, C:R.371, C:H.373 XYP.20: 6 residues within 4Å: Chain C: D.57, I.250, I.310, R.312, Y.336 Ligands: XYP.3 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.57, C:D.57, C:R.312, C:R.312, C:Y.336 Water bridges: C:R.60 Salt bridges: C:R.60 XYP.21: 6 residues within 4Å: Chain C: Q.366, H.368, H.369, R.389, S.391, K.392 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Q.366, C:S.391, C:S.391, C:K.392 Water bridges: C:H.368, C:R.389, C:R.389, C:R.389 Salt bridges: C:H.368, C:R.389 XYP.22: 7 residues within 4Å: Chain C: Y.134, V.136, P.145, Q.146, R.148, T.168, V.171 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.146, C:Q.146, C:T.168 Salt bridges: C:R.148 XYP.26: 6 residues within 4Å: Chain C: T.211, N.299 Chain D: T.211, W.245, E.269, N.299 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:N.299, C:T.211, C:T.211, C:N.299 Water bridges: D:T.211, C:T.211, C:T.211, C:K.305, C:K.305 XYP.27: 13 residues within 4Å: Chain D: W.113, P.233, Q.289, H.352, E.353, K.358, H.360, W.380, D.382, W.383, E.405, V.406, R.450 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:Q.289, D:K.358, D:H.360, D:W.383, D:E.405, D:E.405, D:R.450, D:R.450 Salt bridges: D:H.352, D:K.358 XYP.28: 6 residues within 4Å: Chain D: K.163, H.339, Y.341, R.371, H.373, D.559 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:K.163, D:K.163, D:H.373 Water bridges: D:K.163, D:Y.341, D:R.371, D:R.371, D:H.373 XYP.29: 6 residues within 4Å: Chain B: D.57, K.58 Chain D: T.584, K.585, E.604 Ligands: XYP.13 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Water bridges: B:K.58, D:E.604 Hydrogen bonds: D:K.585, D:E.604 Salt bridges: D:K.585 XYP.30: 8 residues within 4Å: Chain B: K.603 Chain D: D.57, R.60, I.250, I.310, R.312, Y.336 Ligands: XYP.12 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:K.603, D:D.57 Water bridges: D:R.60, D:R.312 Salt bridges: D:R.312 XYP.31: 7 residues within 4Å: Chain D: Y.134, V.136, P.145, Q.146, R.148, T.168, V.171 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.146, D:Q.146, D:T.168 Water bridges: D:D.141 Salt bridges: D:R.148 XYP.32: 5 residues within 4Å: Chain D: S.419, K.483, L.555, A.556, I.557 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.483, D:K.483, D:I.557 Water bridges: D:N.397, D:I.557 XYP.33: 7 residues within 4Å: Chain D: Q.366, H.368, H.369, R.389, S.391, K.392, D.613 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.366, D:S.391, D:S.391, D:K.392 Water bridges: D:Q.366, D:T.609 Salt bridges: D:H.368, D:R.389

9 x XYS: alpha-D-xylopyranose(Non-covalent)

XYS.8: 6 residues within 4Å: Chain A: N.397, N.398, N.399, S.420, E.421 Ligands: XYS.9 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.397, A:N.397, A:N.398, A:E.421, A:E.421 Water bridges: A:N.397, A:N.399 XYS.9: 9 residues within 4Å: Chain A: V.160, P.161, K.163, L.345, D.374, N.397, N.398, N.399 Ligands: XYS.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.163, A:D.374, A:C.375, A:N.399, A:N.399 Water bridges: A:R.347 XYS.16: 11 residues within 4Å: Chain B: V.160, P.161, K.163, L.345, R.347, D.374, C.375, N.397, N.398, N.399 Ligands: XYS.17 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.347, B:R.347, B:D.374, B:N.397, B:N.397, B:N.399, B:N.399, B:N.399 Water bridges: B:K.163, B:K.163, B:K.163 Salt bridges: B:K.163 XYS.17: 6 residues within 4Å: Chain B: N.397, N.398, N.399, S.420, E.421 Ligands: XYS.16 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.397, B:N.397, B:N.398, B:E.421, B:E.421, B:E.421 Water bridges: B:N.397, B:N.399 XYS.23: 6 residues within 4Å: Chain C: N.397, N.398, N.399, S.420, E.421 Ligands: XYS.24 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.397, C:N.397, C:N.398, C:E.421, C:E.421, C:E.421 Water bridges: C:N.397, C:N.399 XYS.24: 10 residues within 4Å: Chain C: V.160, P.161, K.163, L.345, R.347, D.374, C.375, N.397, N.399 Ligands: XYS.23 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.347, C:R.347, C:N.397, C:N.397, C:N.399, C:N.399, C:N.399 Water bridges: C:K.163 XYS.25: 6 residues within 4Å: Chain A: D.57, K.58 Chain C: T.584, K.585, E.604 Ligands: XYP.4 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Water bridges: A:D.57, A:D.57, C:E.604, C:E.604 Hydrogen bonds: C:K.585 XYS.34: 10 residues within 4Å: Chain D: V.160, P.161, K.163, L.345, R.347, D.374, C.375, N.397, N.399 Ligands: XYS.35 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.347, D:R.347, D:D.374, D:N.397, D:N.397, D:N.399, D:N.399, D:N.399 Water bridges: D:K.163 XYS.35: 6 residues within 4Å: Chain D: N.397, N.398, N.399, S.420, E.421 Ligands: XYS.34 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.397, D:N.397, D:N.398, D:E.421, D:E.421, D:E.421 Water bridges: D:N.399

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, C.H. et al., The substrate/product-binding modes of a novel GH120 beta-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485. Biochem.J. (2012)

Release Date

2013-02-27

Peptides

Xylosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Xylosidase

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