SMTL ID : 7b0p.2 (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

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

OLC.1: 13 residues within 4Å: Chain A: F.37, T.41, H.104, V.108, L.112, F.152, L.156, S.167, F.171, H.172, F.199, I.206 Ligands: OLC.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.37, A:T.41, A:L.112, A:F.152, A:L.156, A:L.156, A:F.171, A:F.171, A:I.206 Hydrogen bonds: A:H.104 OLC.2: 16 residues within 4Å: Chain A: V.45, H.104, F.105, V.108, I.160, F.164, S.167, F.168, F.171, W.181, I.191, L.194, F.199, A.202, I.206 Ligands: OLC.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.45, A:I.160, A:F.164, A:F.168, A:F.171, A:I.206 Hydrogen bonds: A:W.181 Salt bridges: A:H.104 OLC.3: 10 residues within 4Å: Chain A: L.39, M.42, Y.46, S.83, P.84, Q.116, M.119, Y.120, I.123 Ligands: OLC.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.39, A:M.42, A:Y.120, A:Y.120, A:I.123 Hydrogen bonds: A:S.83 OLC.4: 5 residues within 4Å: Chain A: G.47, K.48, W.49 Ligands: OLC.3, OLC.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.48, A:W.49 OLC.5: 8 residues within 4Å: Chain A: I.36, L.39, A.40, A.43, L.134, F.209, G.213 Ligands: OLC.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.36, A:L.39, A:L.39, A:A.43, A:L.134, A:F.209 OLC.6: 9 residues within 4Å: Chain A: W.49, H.201, C.204, A.205, L.208, F.209, G.212, I.215 Ligands: OLC.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.208, A:L.208, A:F.209, A:F.209 Hydrogen bonds: A:H.201 OLC.7: 7 residues within 4Å: Chain A: W.49, L.50, Y.52, F.53, F.57, H.201 Ligands: OLC.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.49, A:W.49, A:W.49, A:Y.52, A:Y.52, A:F.53, A:F.53, A:F.53 Hydrogen bonds: A:H.201

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: S.98, T.99, N.100, K.187 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.100, A:N.100, A:K.187 GOL.9: 2 residues within 4Å: Chain A: K.114, Y.117 No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain A: S.146, I.147, S.214, Y.218 Ligands: PG5.12 No protein-ligand interaction detected (PLIP) GOL.11: 2 residues within 4Å: Chain A: D.179, Y.180 No protein-ligand interaction detected (PLIP)

1 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.12: 4 residues within 4Å: Chain A: I.147, I.150, I.154 Ligands: GOL.10 No protein-ligand interaction detected (PLIP)

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
B

Membrane

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

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