SMTL ID : 8p7e.1

Crystal structure of the lipase SpL from Sphingomonas sp. HXN-200 in complex with benzylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

12 x ABN: BENZYLAMINE(Non-covalent)(Non-functional Binders)

ABN.1: 15 residues within 4Å: Chain A: M.54, G.105, G.106, G.107, D.172, S.173, A.174, Y.202, L.222, L.223, S.227, F.231, H.295, G.296 Ligands: ABN.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.222, A:F.231 Hydrogen bonds: A:G.106, A:S.173, A:H.295 ABN.2: 10 residues within 4Å: Chain A: W.108, N.177, A.204, T.206, T.207, G.232, Y.235, A.237, A.244 Ligands: ABN.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.108, A:W.108, A:T.207, A:Y.235, A:A.237 Water bridges: A:T.207, A:G.232 ABN.3: 14 residues within 4Å: Chain A: G.106, G.107, W.108, S.173, A.174, A.204, L.223, M.228, F.231, G.232, L.267, H.295 Ligands: ABN.1, ABN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.108, A:M.228, A:F.231, A:L.267 Hydrogen bonds: A:G.107, A:S.173, A:A.174 ABN.4: 9 residues within 4Å: Chain A: E.72, D.73, R.74, I.85, R.86, L.87, I.132, W.157, I.162 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.72, A:R.74, A:I.85, A:I.85, A:L.87 ABN.5: 12 residues within 4Å: Chain B: M.42, M.54, M.57, G.106, G.107, I.110, L.222, L.223, S.227, F.231, H.295, G.296 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.107 ABN.6: 13 residues within 4Å: Chain B: G.106, G.107, W.108, S.173, A.174, A.204, L.223, M.228, F.231, G.232, L.267, H.295 Ligands: ABN.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.108, B:M.228, B:F.231, B:L.267, B:L.267 Hydrogen bonds: B:G.107, B:S.173, B:A.174 ABN.7: 10 residues within 4Å: Chain B: W.108, N.177, A.204, T.206, T.207, G.232, Y.235, A.237, A.244 Ligands: ABN.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.108, B:W.108, B:T.207, B:Y.235, B:Y.235, B:A.237 Water bridges: B:G.232 ABN.8: 1 residues within 4Å: Ligands: ABN.9 No protein-ligand interaction detected (PLIP) ABN.9: 2 residues within 4Å: Chain B: P.25 Ligands: ABN.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.25, B:P.25 ABN.10: 8 residues within 4Å: Chain B: F.30, F.33, L.60, A.61, Q.302, G.303, P.305 Ligands: ABN.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.302 ABN.11: 5 residues within 4Å: Chain B: A.29, F.30, F.33, G.303 Ligands: ABN.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.29, B:F.33 ABN.12: 9 residues within 4Å: Chain B: E.72, D.73, R.74, I.85, R.86, L.87, I.132, W.157, I.162 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.72, B:R.74, B:I.85, B:L.87 Hydrogen bonds: B:E.72 Water bridges: B:R.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zukic, E. et al., Biocatalytic Heteroaromatic Amide Formation in Water Enabled by a Catalytic Tetrad and Two Access Tunnels. Acs Catalysis (2024)

Release Date

2024-06-12

Peptides

Lipase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lipase

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