SMTL ID : 6khl.1

Lipase (Blocked form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x DK0: (2~{R})-1-phenylpropan-2-ol(Covalent)

DK0.1: 13 residues within 4Å: Chain A: G.37, L.38, S.114, W.115, V.140, F.176, F.179, W.192, F.211, H.285 Ligands: GOL.4, GOL.8, GOL.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.38, A:L.38, A:V.140, A:F.176, A:F.179, A:W.192, A:F.211, A:F.211 Hydrogen bonds: A:L.38, A:W.115 DK0.10: 12 residues within 4Å: Chain B: G.37, L.38, S.114, W.115, V.140, F.176, F.179, W.192, F.211, H.285 Ligands: GOL.14, GOL.15 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.38, B:L.38, B:V.140, B:F.176, B:F.179, B:W.192, B:F.211, B:F.211 Hydrogen bonds: B:L.38, B:W.115

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: Q.142, N.231, Y.236, V.264, R.267 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.142, A:N.231, A:Y.236, A:R.267 Water bridges: A:R.121 GOL.3: 4 residues within 4Å: Chain A: R.69, Q.73 Chain B: R.69, Q.73 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.69, A:R.69, B:R.69, B:R.69 Water bridges: A:Q.18, A:Q.18, A:Q.73, A:Q.73, B:Q.18, B:Q.18, B:Q.73 GOL.4: 6 residues within 4Å: Chain A: F.179, P.189, W.192, F.211 Ligands: DK0.1, GOL.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.176, A:F.179 GOL.5: 5 residues within 4Å: Chain A: N.210, F.211, G.212, A.213, P.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.210, A:N.210, A:F.211 GOL.8: 7 residues within 4Å: Chain A: G.39, N.210, F.211, G.212, A.213 Ligands: DK0.1, GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.210, A:G.212, A:A.213 GOL.9: 11 residues within 4Å: Chain A: G.37, L.38, G.39, E.40, H.113, S.114, H.203, F.211, H.285, E.286 Ligands: DK0.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.38, A:S.114, A:H.203, A:E.286 GOL.13: 8 residues within 4Å: Chain B: P.143, R.144, G.178, F.179, D.181, P.253, D.256, F.257 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.144, B:R.144, B:P.253 Water bridges: B:D.181, B:D.181 GOL.14: 7 residues within 4Å: Chain B: G.39, N.210, F.211, G.212, A.213 Ligands: DK0.10, GOL.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.210, B:G.212, B:A.213, B:A.213 GOL.15: 11 residues within 4Å: Chain B: G.37, L.38, G.39, E.40, H.113, S.114, H.203, F.211, H.285, E.286 Ligands: DK0.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.38, B:H.113, B:S.114, B:H.203 GOL.16: 5 residues within 4Å: Chain A: M.72, K.207, F.208 Chain B: Q.4, E.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.5, B:E.5 GOL.17: 4 residues within 4Å: Chain B: F.176, P.189, W.192 Ligands: GOL.14 No protein-ligand interaction detected (PLIP)

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

PEG.6: 9 residues within 4Å: Chain A: H.41, R.44, V.199, D.202, D.206, N.289 Chain B: A.2, L.3, V.25 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:A.2, B:A.2, A:N.289 Water bridges: A:R.44, A:D.206, A:D.206 PEG.7: 10 residues within 4Å: Chain A: V.76, W.77, A.78, D.79, T.164, D.165, P.166, P.214, M.215, S.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.77, A:T.164 Water bridges: A:D.79 PEG.11: 6 residues within 4Å: Chain B: D.104, D.105, L.106, P.107, D.132, V.308 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.104, B:V.308 Water bridges: B:R.130 PEG.12: 8 residues within 4Å: Chain A: A.2, L.3, V.25 Chain B: R.44, V.199, D.202, D.206, N.289 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:R.44, B:R.44, B:D.206 Hydrogen bonds: A:A.2, A:A.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, H.J. et al., Closed, blocked, and open states of lipase from type II Cutibacterium acnes. To Be Published

Release Date

2020-07-22

Peptides

Hydrolase, alpha/beta domain protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hydrolase, alpha/beta domain protein

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