SMTL ID : 1r85.1

Crystal structure of the extracellular xylanase from Geobacillus stearothermophilus T-6 (XT6): The WT enzyme (monoclinic form) at 1.45A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

7 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 4 residues within 4Å: Chain A: H.11, D.365 Ligands: CL.8, GOL.30 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.11, A:D.365 ZN.2: 2 residues within 4Å: Chain A: D.21 Ligands: GOL.27 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.21, H2O.9, H2O.9, H2O.9, H2O.9, H2O.9 ZN.3: 2 residues within 4Å: Chain A: D.282 Ligands: ZN.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.282, A:D.282, H2O.12 ZN.4: 4 residues within 4Å: Chain A: E.35, E.58, H.322 Ligands: CL.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.58, A:E.58, A:H.322, H2O.1 ZN.5: 4 residues within 4Å: Chain A: E.27, S.307, I.310 Ligands: GOL.22 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.27, A:S.307, A:I.310, H2O.5 ZN.6: 4 residues within 4Å: Chain A: D.297, A.374, D.377, K.379 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.297, A:A.374, A:D.377, A:K.379, H2O.2 ZN.7: 2 residues within 4Å: Ligands: ZN.3, GOL.30 No protein-ligand interaction detected (PLIP)

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

CL.8: 4 residues within 4Å: Chain A: H.11, D.365 Ligands: ZN.1, GOL.30 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: E.58, H.322, W.324 Ligands: ZN.4, GOL.25 Ligand excluded by PLIP

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

SO4.10: 2 residues within 4Å: Chain A: P.285, K.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.284, A:K.286 Water bridges: A:Q.287 SO4.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.12: 5 residues within 4Å: Chain A: G.89, M.90, D.91 Ligands: GOL.16, GOL.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.91 Water bridges: A:M.90, A:D.91

19 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 6 residues within 4Å: Chain A: D.21, Q.22, K.25, N.53 Ligands: GOL.27, GOL.31 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain A: P.279, A.283, V.339 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: P.275, R.328, D.330 Ligands: GOL.17 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain A: K.148, D.149, D.150, I.151, K.152, N.195 Ligands: SO4.12 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain A: P.274, Y.332, Y.347, K.352 Ligands: GOL.15 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain A: Y.203, N.204, W.273 Ligands: GOL.20 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain A: Y.333, G.337, K.349, E.351 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain A: Y.203, H.236, W.324, R.328 Ligands: GOL.18 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain A: G.165, K.166, L.167, A.213 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain A: E.27, F.28, S.307, D.308, I.310, S.311 Ligands: ZN.5 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain A: E.58, E.159, Q.234, E.265, W.316, W.324 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain A: L.133, K.134, E.137, V.183 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain A: N.321, H.322, T.323, W.324, D.326 Ligands: CL.9 Ligand excluded by PLIP GOL.26: 1 residues within 4Å: Chain A: E.70 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain A: K.49, N.88 Ligands: ZN.2, GOL.13 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain A: E.70, K.111, L.131, R.135 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain A: G.162, D.163, D.164, R.168 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain A: Y.281, P.364, D.365 Ligands: ZN.1, ZN.7, CL.8 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain A: T.29, N.53, G.89, D.91 Ligands: SO4.12, GOL.13 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zolotnitsky, G. et al., Mapping glycoside hydrolase substrate subsites by isothermal titration calorimetry. Proc.Natl.Acad.Sci.Usa (2004)

Release Date

2004-07-20

Peptides

Endo-1,4-beta-xylanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endo-1,4-beta-xylanase

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