SMTL ID : 7wol.1

Crystal structure of lipase TrLipB from Thermomocrobium roseum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.1: 7 residues within 4Å: Chain A: G.92, G.93, G.94, S.165, A.166, W.215, H.293 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.93, A:G.94, A:S.165, A:A.166 Salt bridges: A:H.293, A:H.293 SIN.12: 9 residues within 4Å: Chain B: G.92, G.93, G.94, S.165, A.166, W.215, H.293, G.294, F.298 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.93, B:G.94, B:S.165, B:A.166 Salt bridges: B:H.293, B:H.293

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: R.33, Q.37, R.40, M.97, G.98, A.99, L.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.37, A:R.40, A:G.98 GOL.5: 5 residues within 4Å: Chain A: D.218, L.221, I.222, R.225 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.218, A:R.225, A:R.225 GOL.6: 6 residues within 4Å: Chain A: R.199, A.244, R.245, A.246, D.247, R.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.199, A:R.199, A:A.246 GOL.8: 8 residues within 4Å: Chain A: L.176, R.179, D.180, P.239, Y.240, A.246, D.247, D.248 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.179, A:Y.240, A:D.247, A:D.248 GOL.19: 6 residues within 4Å: Chain B: A.178, R.179, G.182, E.183, V.184, P.185 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.179, B:G.182, B:V.184, B:V.184 Water bridges: B:E.183

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

PEG.3: 5 residues within 4Å: Chain A: P.132, E.136, L.177, R.181, Y.240 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.181 PEG.4: 2 residues within 4Å: Chain A: T.68, M.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.69 PEG.13: 7 residues within 4Å: Chain B: G.98, A.99, D.122, Y.123, R.124, L.125 Ligands: EDO.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.98, B:D.122 Water bridges: B:L.125 PEG.15: 4 residues within 4Å: Chain B: P.132, E.136, R.181, Y.240 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.240, B:Y.240

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

EDO.7: 4 residues within 4Å: Chain A: R.217, L.221 Ligands: GOL.5, EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.217 Water bridges: A:R.217 EDO.9: 6 residues within 4Å: Chain A: R.199, R.217, L.221, E.231, P.232 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.199, A:R.217, A:E.231, A:E.231 EDO.10: 8 residues within 4Å: Chain A: R.76, P.77, V.80, T.81, G.82, L.84, L.152, G.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.76, A:P.77, A:G.82 EDO.11: 4 residues within 4Å: Chain A: R.124, L.125, E.128, H.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.125 Water bridges: A:H.129 EDO.14: 4 residues within 4Å: Chain B: R.199, A.244, R.245, R.275 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.199, B:R.199 EDO.16: 7 residues within 4Å: Chain B: R.179, D.180, P.239, Y.240, A.246, D.247, D.248 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.179, B:D.180, B:D.247, B:D.248 EDO.17: 4 residues within 4Å: Chain B: V.186, G.251, P.253, P.254 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.186 Water bridges: B:L.252 EDO.18: 4 residues within 4Å: Chain B: R.33, M.97, G.98 Ligands: PEG.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.98 EDO.20: 5 residues within 4Å: Chain B: R.187, F.188, P.254, R.318, A.319 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.187, B:R.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fang, Y. et al., Crystal structure of lipase TrLipB from Thermomocrobium roseum. To Be Published

Release Date

2023-01-25

Peptides

Lipase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lipase