SMTL ID : 6nkf.1 (1 other biounit)

Crystal Structure of the Lipase Lip_vut4 from Goat Rumen metagenome.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: K.52, Q.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.55 EDO.3: 6 residues within 4Å: Chain A: I.192, F.193, D.194, N.199, S.200 Ligands: PEG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.194, A:N.199 EDO.4: 10 residues within 4Å: Chain A: G.68, W.69, S.140, S.141, P.180, H.195, P.201, E.202, V.244 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.68, A:S.141 EDO.5: 8 residues within 4Å: Chain A: G.66, C.67, G.68, S.140, V.243, H.273 Chain B: M.45 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.66, A:G.68, A:S.140 Water bridges: A:C.67 EDO.6: 5 residues within 4Å: Chain A: F.49, R.51 Chain B: I.192, D.242, V.243 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.51 Water bridges: B:D.242, B:H.273 EDO.7: 4 residues within 4Å: Chain A: E.25, Y.26, T.27, F.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.25 Water bridges: A:E.25, A:E.25 EDO.9: 7 residues within 4Å: Chain B: P.180, H.195, P.201, E.202, V.243, V.244 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.202 Water bridges: B:S.141 EDO.10: 4 residues within 4Å: Chain B: Q.55, T.57, A.125, N.128 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.128 EDO.11: 8 residues within 4Å: Chain A: M.45 Chain B: G.66, C.67, G.68, S.140, V.243, H.273 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.66, B:G.68, B:S.140 Water bridges: B:C.67 EDO.12: 6 residues within 4Å: Chain B: F.193, D.194, S.197, N.199, S.200 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.194, B:S.197, B:S.197 EDO.13: 5 residues within 4Å: Chain B: W.71, F.193, N.199, K.204 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.204, B:K.204 EDO.14: 3 residues within 4Å: Chain A: L.48 Chain B: W.71, T.72 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.71, B:T.72

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

PEG.2: 5 residues within 4Å: Chain A: W.71, I.192, F.193 Chain B: F.49 Ligands: EDO.3 No protein-ligand interaction detected (PLIP)

1 x SBT: 2-BUTANOL(Non-covalent)

SBT.8: 9 residues within 4Å: Chain A: L.20, P.22, H.37, S.77 Chain B: L.20, P.22, H.37, S.77, I.80 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.20, A:P.22, B:L.20, B:I.80 Hydrogen bonds: B:S.77, B:S.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of the Lipase Lip_vut4 from Goat Rumen metagenome. To Be Published

Release Date

2020-01-22

Peptides

Lip_vut4, C3L: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Lip_vut4, C3L

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