SMTL ID : 7b0q.1

In meso structure of the membrane integral lipoprotein intramolecular transacylase Lit from Bacillus cereus with H85A mutation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: S.98, T.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.99, A:T.99 Water bridges: A:N.100 GOL.2: 2 residues within 4Å: Chain A: N.110, K.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.110, A:N.110, A:K.114 Water bridges: A:K.114 GOL.3: 5 residues within 4Å: Chain A: L.50, H.201, C.204, A.205, L.208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.204

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

OLC.4: 6 residues within 4Å: Chain A: R.22, L.23, L.26, H.144, L.148 Ligands: PG5.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.22, A:L.23, A:L.26 OLC.5: 10 residues within 4Å: Chain A: I.36, A.40, A.43, V.127, L.142, F.209, G.213, C.217 Ligands: OLC.8, OLC.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.36, A:V.127, A:L.142, A:F.209 OLC.6: 12 residues within 4Å: Chain A: F.37, V.108, I.111, M.157, F.183, I.191, L.194, E.196, F.199, A.203, I.206 Ligands: OLC.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.37, A:F.37, A:V.108, A:I.111, A:F.199, A:I.206 Hydrogen bonds: A:L.194 OLC.7: 15 residues within 4Å: Chain A: V.45, L.78, N.100, G.101, A.104, F.105, W.181, V.182, D.188, I.191, F.199, A.202, A.203, I.206 Ligands: OLC.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.78, A:F.199, A:F.199, A:F.199, A:A.202, A:A.203, A:I.206 Hydrogen bonds: A:D.188 OLC.8: 10 residues within 4Å: Chain A: S.35, L.39, M.42, A.43, Y.46, G.47, A.126 Ligands: OLC.5, OLC.9, OLC.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.39, A:A.43, A:A.126 OLC.9: 10 residues within 4Å: Chain A: A.43, V.44, Y.46, G.47, K.48, W.49, L.50, A.205 Ligands: OLC.5, OLC.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.48, A:W.49, A:W.49 OLC.10: 9 residues within 4Å: Chain A: Y.46, F.85, Q.116, Y.117, M.119, Y.120, I.123, M.124 Ligands: OLC.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.117, A:Y.120, A:I.123

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.11: 4 residues within 4Å: Chain A: P.61, D.62, D.65, M.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.65, A:D.65 CIT.12: 3 residues within 4Å: Chain A: K.68, K.72, R.73 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.68 Salt bridges: A:K.68, A:K.72, A:K.72, A:R.73

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

PG5.13: 4 residues within 4Å: Chain A: R.22, L.26, Y.30 Ligands: OLC.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.22

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