SMTL ID : 6aae.1

Crystal structure of Chloramphenicol-Metabolizaing Enzyme EstDL136

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

6 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.1: 11 residues within 4Å: Chain A: G.81, T.90, D.152, S.153, Y.202, L.203, H.279, G.280, S.283 Chain B: F.34 Ligands: 1PE.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.152, A:S.153, A:S.283 Water bridges: A:G.82, A:S.204, A:S.283 1PE.2: 5 residues within 4Å: Chain A: E.47, W.132, N.136, T.139, L.140 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.47 1PE.6: 12 residues within 4Å: Chain A: M.14, F.34 Chain B: G.81, I.85, D.152, S.153, Y.202, L.203, F.211, H.279, S.283 Ligands: PEG.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.153 Water bridges: B:G.81, B:S.283 1PE.7: 11 residues within 4Å: Chain A: L.10, M.13, M.284, A.287 Chain B: L.10, M.13, M.14, A.38, E.286, A.287 Ligands: 1PE.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.286 1PE.8: 8 residues within 4Å: Chain B: D.67, D.69, Q.100, K.101, S.102, G.103, K.303 Ligands: PEG.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.303 Water bridges: B:D.69 1PE.9: 5 residues within 4Å: Chain B: P.115, E.116, Y.117, R.118, H.214 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.118

13 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: E.8, L.11, Q.12 Chain B: E.200, Y.201 No protein-ligand interaction detected (PLIP) PEG.4: 4 residues within 4Å: Chain A: Q.100, K.101, W.292, E.296 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.101, A:E.296 PEG.5: 5 residues within 4Å: Chain A: D.206, R.209, W.210, G.213 Chain B: F.22 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.209 PEG.10: 5 residues within 4Å: Chain A: A.25 Chain B: G.207, W.210, F.211 Ligands: 1PE.6 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.202, B:S.204, B:G.207 PEG.11: 5 residues within 4Å: Chain B: Q.100, K.101, E.296 Ligands: 1PE.8, PEG.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.101, B:E.296 PEG.12: 6 residues within 4Å: Chain B: N.36, Q.100, K.101, W.292, E.296 Ligands: PEG.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.101 PEG.13: 2 residues within 4Å: Chain B: Y.201, Y.248 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.248 Water bridges: B:E.247, B:Y.248 PEG.14: 2 residues within 4Å: Chain B: D.270, R.304 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.304 Water bridges: B:P.268, B:D.270 PEG.15: 6 residues within 4Å: Chain B: R.56, R.112, P.120, A.121, E.124, D.128 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.56, B:R.112 Water bridges: B:R.56, B:Y.119, B:A.121, B:E.124, B:D.128 PEG.16: 10 residues within 4Å: Chain B: R.45, V.64, P.65, E.66, A.68, D.69, E.70, P.72, L.140, G.141 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.45, B:R.45, B:P.65, B:A.68, B:L.140 PEG.17: 4 residues within 4Å: Chain B: A.271, A.272, W.294, R.297 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.271, B:R.297, B:R.297 Water bridges: B:T.273 PEG.18: 6 residues within 4Å: Chain A: V.46, N.48, R.96 Chain B: V.46, N.48, R.61 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:V.46, B:N.48 Water bridges: B:R.96, A:V.46, A:N.48, A:R.96 PEG.19: 10 residues within 4Å: Chain B: A.166, R.167, G.171, P.172, A.173, L.174, G.237, L.238, A.239, P.240 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S.H. et al., Crystal structure of chloramphenicol-metabolizing enzyme EstDL136 from a metagenome. PLoS ONE (2019)

Release Date

2019-02-06

Peptides

Esterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Esterase