SMTL ID : 4c01.1

Complete crystal structure of carboxylesterase Cest-2923 (lp_2923) from Lactobacillus plantarum WCFS1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

ACT.1: 6 residues within 4Å: Chain A: G.42, G.43, G.44, S.116, A.117, H.233 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.43, A:G.44, A:S.116, A:A.117 Salt bridges: A:H.233 ACT.7: 5 residues within 4Å: Chain B: G.43, G.44, S.116, A.117, H.233 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.43, B:G.44, B:S.116, B:A.117 Water bridges: B:S.203 Salt bridges: B:H.233 ACT.12: 6 residues within 4Å: Chain C: G.42, G.43, G.44, S.116, A.117, H.233 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.43, C:G.44, C:S.116, C:A.117 Salt bridges: C:H.233 ACT.17: 7 residues within 4Å: Chain D: G.42, G.43, G.44, S.116, A.117, F.163, H.233 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.43, D:G.44, D:S.116, D:A.117 Salt bridges: D:H.233 ACT.22: 5 residues within 4Å: Chain E: G.43, G.44, S.116, A.117, H.233 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.43, E:G.44, E:S.116, E:A.117 Salt bridges: E:H.233 ACT.27: 5 residues within 4Å: Chain F: G.43, G.44, S.116, A.117, H.233 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.43, F:G.44, F:S.116, F:A.117 Water bridges: F:E.52, F:S.203 Salt bridges: F:H.233

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

SO4.2: 4 residues within 4Å: Chain A: K.244, K.247, K.249, Y.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.250 Salt bridges: A:K.244, A:K.247, A:K.249 SO4.8: 4 residues within 4Å: Chain B: K.244, K.247, K.249, Y.250 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.244, B:K.247, B:K.249 SO4.13: 3 residues within 4Å: Chain B: T.7 Chain C: T.7 Chain F: T.7 7 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C, 2 interactions with chain F Hydrogen bonds: B:T.7, C:T.7, F:T.7, F:T.7 Water bridges: B:Q.5, C:Q.5, C:Q.5 SO4.14: 2 residues within 4Å: Chain C: R.109, A.273 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.109 SO4.18: 4 residues within 4Å: Chain D: K.244, K.247, K.249, Y.250 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.250 Water bridges: D:K.244 Salt bridges: D:K.244, D:K.247, D:K.249 SO4.19: 2 residues within 4Å: Chain D: R.109, A.273 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.109 SO4.23: 3 residues within 4Å: Chain A: T.7 Chain D: T.7 Chain E: T.7 8 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D, 3 interactions with chain E Hydrogen bonds: A:T.7, A:T.7, D:T.7, D:T.7, D:T.7, E:T.7, E:T.7 Water bridges: E:Q.5 SO4.24: 5 residues within 4Å: Chain B: E.29 Chain E: K.244, K.247, K.249, Y.250 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Y.250, E:Y.250 Water bridges: E:K.244 Salt bridges: E:K.244, E:K.247, E:K.249

5 x QY9: phenyl acetate(Non-covalent)

QY9.3: 7 residues within 4Å: Chain A: R.6, W.95, T.98, Q.99 Chain E: Q.5, Q.16, N.71 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:Q.16, E:N.71 Salt bridges: A:R.6 QY9.9: 7 residues within 4Å: Chain B: Q.5, Q.16, N.71 Chain C: R.6, T.98, Q.99 Ligands: CCN.11 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:N.71 Water bridges: E:S.26 QY9.15: 7 residues within 4Å: Chain C: Q.5, Q.16, H.48, E.53, N.71 Chain F: R.6, Q.99 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:H.48 Hydrogen bonds: C:Q.16 Water bridges: C:Q.5, C:T.18 QY9.25: 8 residues within 4Å: Chain D: Q.5, Q.16, N.71 Chain E: R.6, W.95, T.98, Q.99 Ligands: CCN.20 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Salt bridges: E:R.6 Hydrogen bonds: D:N.71 QY9.28: 7 residues within 4Å: Chain B: R.6, T.98, Q.99 Chain F: Q.5, Q.16, N.71 Ligands: CCN.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.98, B:Q.99 Salt bridges: B:R.6

12 x CCN: ACETONITRILE(Non-functional Binders)

CCN.4: 5 residues within 4Å: Chain A: D.201, E.202, S.203, I.232, H.233 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.202, A:I.232 Hydrogen bonds: A:D.201, A:E.202, A:S.203, A:H.233 CCN.5: 3 residues within 4Å: Chain A: Q.5, Q.16 Chain D: Q.99 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.99, A:Q.5 Water bridges: D:R.6 CCN.6: 4 residues within 4Å: Chain A: Y.47, H.48, N.71 Chain D: T.98 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.47, D:T.98 Water bridges: A:N.71 CCN.10: 5 residues within 4Å: Chain B: D.201, E.202, S.203, I.232, H.233 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.232 Hydrogen bonds: B:E.202, B:S.203, B:H.233 CCN.11: 5 residues within 4Å: Chain B: Y.47, H.48, N.71 Chain C: T.98 Ligands: QY9.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.47, C:T.98 Hydrogen bonds: B:H.48 CCN.16: 5 residues within 4Å: Chain C: D.201, E.202, S.203, I.232, H.233 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:E.202, C:I.232 Hydrogen bonds: C:E.202, C:S.203, C:H.233 CCN.20: 4 residues within 4Å: Chain D: Y.47, H.48, N.71 Ligands: QY9.25 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.47 Water bridges: D:N.71, D:N.71 CCN.21: 5 residues within 4Å: Chain D: D.201, E.202, S.203, I.232, H.233 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:E.202 Hydrogen bonds: D:D.201, D:E.202, D:S.203, D:H.233 CCN.26: 5 residues within 4Å: Chain E: D.201, E.202, S.203, I.232, H.233 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:E.202, E:I.232 Hydrogen bonds: E:D.201, E:E.202, E:S.203, E:H.233 CCN.29: 5 residues within 4Å: Chain F: D.201, E.202, S.203, I.232, H.233 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:I.232 Hydrogen bonds: F:E.202, F:S.203, F:H.233 CCN.30: 4 residues within 4Å: Chain F: Y.47, H.48, N.71 Ligands: QY9.28 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:Y.47 Hydrogen bonds: F:H.48 Water bridges: F:N.71, F:N.71 CCN.31: 5 residues within 4Å: Chain B: R.6, N.9 Chain F: F.15, Q.16, N.71 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain F Hydrophobic interactions: B:N.9, F:Q.16 Hydrogen bonds: F:Q.16, F:N.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benavente, R. et al., Structure, Biochemical Characterization and Analysis of the Pleomorphism of Carboxylesterase Cest-2923 from Lactobacillus Plantarum Wcfs1. FEBS J. (2013)

Release Date

2013-10-30

Peptides

CEST-2923: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

CEST-2923

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