SMTL ID : 6fkx.1

Crystal structure of an acetyl xylan esterase from a desert metagenome

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

hetero-1-4-1-mer

Ligands

6 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: L.172, A.173, M.174, V.177, P.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.173 NA.4: 5 residues within 4Å: Chain B: L.170, A.171, M.172, V.175, P.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.172, B:V.175 NA.8: 5 residues within 4Å: Chain C: L.170, A.171, M.172, V.175, P.177 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.170 NA.12: 5 residues within 4Å: Chain D: L.167, A.168, M.169, V.172, P.174 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.168, D:V.172 NA.16: 5 residues within 4Å: Chain E: L.170, A.171, M.172, V.175, P.177 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.175 NA.19: 5 residues within 4Å: Chain F: L.170, A.171, M.172, V.175, P.177 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:V.175, F:V.175

13 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 6 residues within 4Å: Chain A: E.52, F.53, H.62, K.76, W.103, L.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.52, A:F.53 Salt bridges: A:H.62 MES.5: 3 residues within 4Å: Chain B: V.45, W.62, R.70 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.70 MES.6: 5 residues within 4Å: Chain B: A.49, E.50, F.51, H.60, W.101 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.50, B:E.50, B:F.51 Salt bridges: B:H.60 MES.9: 8 residues within 4Å: Chain C: A.49, E.50, F.51, H.60, H.72, K.74, W.101, L.125 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.50, C:F.51, C:K.74, C:K.74 Salt bridges: C:H.60 MES.10: 4 residues within 4Å: Chain C: V.45, E.47, W.62, R.70 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:E.47, C:R.70 MES.11: 5 residues within 4Å: Chain A: W.137, M.139 Chain C: W.135, M.137, A.138 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Water bridges: C:R.143, C:R.143, A:Y.142, A:R.145 Hydrogen bonds: A:M.139 MES.13: 4 residues within 4Å: Chain D: V.42, E.44, W.59, R.67 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.67 MES.14: 6 residues within 4Å: Chain D: A.46, E.47, F.48, H.57, K.71, W.98 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.47, D:F.48 Water bridges: D:K.71 Salt bridges: D:H.57 MES.15: 5 residues within 4Å: Chain D: W.132, M.134 Chain E: E.129, W.135, M.137 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Water bridges: E:R.143 Hydrogen bonds: D:R.140 MES.17: 5 residues within 4Å: Chain E: A.49, E.50, F.51, H.60, W.101 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.50, E:F.51, E:H.60 Salt bridges: E:H.60 MES.18: 4 residues within 4Å: Chain E: V.45, E.47, W.62, R.70 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.62 Salt bridges: E:R.70 MES.20: 5 residues within 4Å: Chain F: A.49, E.50, F.51, H.60, W.101 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:E.50, F:F.51, F:W.101 Salt bridges: F:H.60 MES.21: 7 residues within 4Å: Chain B: W.135, M.137 Chain F: W.135, S.136, M.137, S.139, R.143 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:R.143, B:W.135 Water bridges: B:R.143

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

SO4.3: 4 residues within 4Å: Chain A: V.47, E.49, W.64, R.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.49 Salt bridges: A:R.72

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 5 residues within 4Å: Chain B: P.200, R.201, I.202, R.265, A.266 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adesioye, F.A. et al., Structural Characterization and Directed Evolution of a Novel Acetyl Xylan Esterase Reveals Thermostability Determinants of the Carbohydrate Esterase 7 Family. Appl. Environ. Microbiol. (2018)

Release Date

2018-02-28

Peptides

Acetyl xylan esterase: A
Acetyl xylan esterase: BCEF
Acetyl xylan esterase: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

E
E

F
F

D
C

Acetyl xylan esterase

Acetyl xylan esterase

Acetyl xylan esterase