SMTL ID : 7b0p.1 (1 other biounit)

In meso structure of the membrane integral lipoprotein intramolecular transacylase Lit from Bacillus cereus in space group P21212

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

5 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.1: 12 residues within 4Å: Chain A: F.37, T.41, H.104, V.108, I.115, V.118, F.171, H.172, L.175, F.176, F.199 Ligands: OLC.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.37, A:T.41, A:I.115, A:V.118 Hydrogen bonds: A:H.104, A:H.172 OLC.2: 17 residues within 4Å: Chain A: L.78, H.104, F.105, V.108, F.164, S.167, F.168, F.171, W.181, I.191, L.194, F.198, F.199, A.203, I.206 Ligands: OLC.1, GOL.14 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.78, A:F.164, A:F.168, A:F.168, A:F.171, A:F.171, A:F.171, A:F.198, A:A.203, A:I.206 Hydrogen bonds: A:W.181 Salt bridges: A:H.104 OLC.3: 8 residues within 4Å: Chain A: I.36, L.39, A.40, A.43, Y.46, F.209 Ligands: OLC.4, GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.36, A:I.36, A:L.39 OLC.4: 13 residues within 4Å: Chain A: L.39, Y.46, I.79, T.80, S.83, P.84, Q.116, M.119, Y.120, I.123, M.124 Ligands: OLC.3, GOL.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.39, A:Y.46, A:Y.120, A:I.123 Hydrogen bonds: A:T.80 OLC.15: 7 residues within 4Å: Chain A: S.146, I.147, I.150, L.211, S.214, I.215, Y.218 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.150, A:L.211, A:L.211, A:I.215, A:Y.218, A:Y.218 Hydrogen bonds: A:Y.218

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: A.33, F.37, L.148, F.152, I.210 No protein-ligand interaction detected (PLIP) GOL.6: 4 residues within 4Å: Chain A: W.49, Y.52, F.53, K.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.72, A:K.72 GOL.7: 5 residues within 4Å: Chain A: G.47, K.48, W.49 Ligands: OLC.3, GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.48, A:W.49 GOL.8: 5 residues within 4Å: Chain A: A.43, G.47, L.50, F.209 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.47, A:L.50 GOL.9: 3 residues within 4Å: Chain A: I.125, I.128, G.129 No protein-ligand interaction detected (PLIP) GOL.10: 3 residues within 4Å: Chain A: H.91, L.92, P.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.91 Water bridges: A:H.91 GOL.11: 4 residues within 4Å: Chain A: I.32, A.126, V.127, F.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.126 GOL.12: 2 residues within 4Å: Chain A: A.121, I.125 No protein-ligand interaction detected (PLIP) GOL.13: 2 residues within 4Å: Chain A: Y.120 Ligands: OLC.4 No protein-ligand interaction detected (PLIP) GOL.14: 4 residues within 4Å: Chain A: L.156, S.167, F.171 Ligands: OLC.2 No protein-ligand interaction detected (PLIP) GOL.16: 2 residues within 4Å: Chain A: G.10, E.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.10, A:E.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olatunji, S. et al., Structural basis of the membrane intramolecular transacylase reaction responsible for lyso-form lipoprotein synthesis. Nat Commun (2021)

Release Date

2021-05-26

Peptides

Hypothetical Membrane Spanning Protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Hypothetical Membrane Spanning Protein

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