SMTL ID : 7b0r.1

In meso structure of the membrane integral lipoprotein intramolecular transacylase Lit from Bacillus cereus with H85R mutation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: A.43, G.47, W.49, L.50, F.209 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.47, A:W.49, A:L.50 GOL.2: 4 residues within 4Å: Chain A: G.47, K.48, W.49 Ligands: GOL.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.48, A:W.49 GOL.6: 2 residues within 4Å: Chain A: K.72, R.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.72, A:R.73, A:R.73

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

OLC.3: 12 residues within 4Å: Chain A: V.45, I.79, L.82, R.104, F.105, F.183, I.191, F.198, F.199, A.202, A.203 Ligands: OLC.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.45, A:I.79, A:L.82, A:F.183, A:F.198, A:F.198, A:F.199, A:A.202, A:A.203 Hydrogen bonds: A:R.104, A:F.183 Salt bridges: A:R.104 OLC.4: 11 residues within 4Å: Chain A: F.37, I.111, L.112, I.115, M.157, E.196, F.199, A.203, I.206, L.207 Ligands: OLC.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.37, A:I.111, A:L.112, A:I.115, A:I.206, A:L.207 OLC.7: 8 residues within 4Å: Chain A: L.39, Y.46, S.83, P.84, Q.116, M.119, Y.120 Ligands: OLC.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.39, A:L.39 Hydrogen bonds: A:S.83, A:Q.116 OLC.8: 9 residues within 4Å: Chain A: I.36, L.39, A.40, A.43, L.142, F.209, G.213, C.217 Ligands: OLC.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.36, A:I.36, A:L.142

1 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.5: 3 residues within 4Å: Chain A: N.110, K.114, Y.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.110, A:K.114

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

CIT.9: 5 residues within 4Å: Chain A: P.61, D.62, D.65, M.66, T.67 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.67 Hydrogen bonds: A:D.65, A:D.65

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

PG5.10: 3 residues within 4Å: Chain A: R.22, L.26, Y.30 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
A

Membrane

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