SMTL ID : 3fyu.1 (1 other biounit)

Crystal structure of acetyl xylan esterase from Bacillus pumilus obtained in presence of D-xylose and sodium acetate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

hetero-4-2-mer

Ligands

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

XYP.1: 5 residues within 4Å: Chain A: Y.47, F.72, D.96 Chain C: S.233, D.234 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.47, A:D.96, C:D.234 Water bridges: A:R.58 XYP.9: 6 residues within 4Å: Chain A: S.233, D.234 Chain C: Y.47, F.72, D.96, G.97 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:Y.47, C:D.96 Water bridges: A:S.233, A:S.233, B:T.306 XYP.16: 4 residues within 4Å: Chain E: Y.47, D.96 Chain F: S.233, D.234 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:D.234 Water bridges: F:S.233, F:S.233, A:T.306

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

EDO.2: 3 residues within 4Å: Chain A: E.299, F.300 Chain E: Y.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.299, A:E.299, A:F.300 EDO.5: 3 residues within 4Å: Chain B: E.299, F.300 Chain C: Y.95 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.299 Water bridges: B:F.300 EDO.6: 4 residues within 4Å: Chain B: Y.47, D.96 Chain D: S.233, D.234 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:T.306 Hydrogen bonds: D:D.234 EDO.12: 3 residues within 4Å: Chain D: E.299, F.300 Chain F: Y.95 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.299 EDO.13: 3 residues within 4Å: Chain B: S.233 Chain D: Y.47, D.96 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.47 EDO.17: 4 residues within 4Å: Chain A: Y.95 Chain C: R.230 Chain E: E.299, F.300 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:E.299, C:R.230 EDO.21: 3 residues within 4Å: Chain D: Y.95 Chain F: E.299, F.300 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.299 EDO.22: 3 residues within 4Å: Chain E: S.233, D.234 Chain F: D.96 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.47, F:D.96

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

CL.3: 4 residues within 4Å: Chain A: P.130, G.141, I.142, L.143 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: I.268, D.269, K.270, G.297, H.298 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: P.130, G.141, I.142, L.143 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain C: P.130, G.141, I.142, L.143 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain C: I.268, D.269, K.270, H.298 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain D: P.130, G.141, I.142, L.143 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain E: P.130, G.141, I.142, L.143 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain E: I.268, K.270, H.298 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain F: P.130, G.141, I.142, L.143 Ligand excluded by PLIP

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.8: 7 residues within 4Å: Chain C: G.90, Y.91, S.181, Q.182, Y.206, P.221, H.298 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.91, C:Y.206, C:P.221 Hydrogen bonds: C:Y.91, C:S.181, C:Q.182 Salt bridges: C:H.298 ACY.15: 8 residues within 4Å: Chain E: G.90, Y.91, S.181, Q.182, Y.206, P.221, I.271, H.298 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:Y.91, E:Y.206, E:P.221, E:I.271 Hydrogen bonds: E:Y.91, E:S.181, E:Q.182 Salt bridges: E:H.298 ACY.20: 7 residues within 4Å: Chain F: G.90, Y.91, S.181, Q.182, P.221, I.271, H.298 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:Y.91, F:P.221, F:I.271 Hydrogen bonds: F:Y.91, F:S.181, F:Q.182 Salt bridges: F:H.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krastanova, I. et al., Structural and functional studies of Bacillus pumilus acetyl xylan esterase. To be Published

Release Date

2010-01-26

Peptides

Acetyl xylan esterase: ACEF
Acetyl xylan esterase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

F
F

B
B

D
D

Acetyl xylan esterase

Acetyl xylan esterase

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