SMTL ID : 2w5f.1 (1 other biounit)

High resolution crystallographic structure of the Clostridium thermocellum N-terminal endo-1,4-beta-D-xylanase 10B (Xyn10B) CBM22-1- GH10 modules complexed with xylohexaose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x XYP- XYP- XYP: beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose

XYP-XYP-XYP.1: 13 residues within 4Å: Chain A: E.222, N.223, K.226, H.265, W.269, Q.272, N.325, N.383, Y.385, Q.415, E.449, W.493, W.501 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.223, A:Q.272

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: N.64, R.65, D.158 Ligands: ACT.3, CD.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.64, A:R.65 ACT.3: 4 residues within 4Å: Chain A: T.156, D.158 Ligands: ACT.2, CD.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.158 ACT.4: 3 residues within 4Å: Chain A: E.24, H.27 Ligands: CD.10 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.27 ACT.5: 6 residues within 4Å: Chain A: N.190, Y.191, K.486, V.487, T.488, A.540 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.486 Hydrogen bonds: A:N.479 Water bridges: A:N.190 ACT.6: 2 residues within 4Å: Chain A: E.115 Ligands: CD.14 No protein-ligand interaction detected (PLIP) ACT.7: 5 residues within 4Å: Chain A: T.335, D.394, C.395, S.398 Ligands: CD.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.394 Hydrogen bonds: A:S.398 Water bridges: A:C.395

8 x CD: CADMIUM ION(Non-covalent)

CD.8: 3 residues within 4Å: Chain A: D.158 Ligands: ACT.2, ACT.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:D.158, A:D.158, ACT.2, ACT.3 CD.9: 5 residues within 4Å: Chain A: T.29, E.31, T.57, R.58, D.162 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.31, A:T.57, A:R.58, H2O.1, H2O.12 CD.10: 3 residues within 4Å: Chain A: E.24, H.27 Ligands: ACT.4 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.24, A:E.24, A:H.27, H2O.1, ACT.4 CD.11: 3 residues within 4Å: Chain A: T.335, C.395 Ligands: ACT.7 5 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: A:C.395, ACT.7, H2O.20, H2O.21, H2O.29 CD.12: 2 residues within 4Å: Chain A: E.116 Ligands: CD.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.116, A:E.116 CD.13: 2 residues within 4Å: Chain A: E.116 Ligands: CD.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.116 CD.14: 2 residues within 4Å: Chain A: E.115 Ligands: ACT.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.115, A:E.115, ACT.6 CD.15: 1 residues within 4Å: Chain A: D.390 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.390, A:D.390, H2O.23, H2O.24, H2O.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Najmudin, S. et al., Putting an N-Terminal End to the Clostridium Thermocellum Xylanase Xyn10B Story: Crystal Structure of the Cbm22-1-Gh10 Modules Complexed with Xylohexaose. J.Struct.Biol. (2010)

Release Date

2010-01-19

Peptides

ENDO-1,4-BETA-XYLANASE Y: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ENDO-1,4-BETA-XYLANASE Y

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