SMTL ID : 7b0o.2 (1 other biounit)

In meso structure of the membrane integral lipoprotein intramolecular transacylase Lit from Bacillus cereus in space group P21

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 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, L.112, K.114, I.115, F.171, H.172, L.175, F.176 Ligands: OLC.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.37, A:T.41, A:L.112, A:L.175 Hydrogen bonds: A:H.104 OLC.2: 18 residues within 4Å: Chain A: V.45, H.104, F.105, V.108, L.156, I.160, F.164, S.167, F.168, F.171, W.181, F.183, I.191, L.194, F.199, A.202, A.203 Ligands: OLC.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.156, A:I.160, A:F.164, A:F.168, A:F.168, A:F.171, A:F.171, A:F.199, A:F.199, A:A.202, A:A.203 Hydrogen bonds: A:W.181 OLC.3: 11 residues within 4Å: Chain A: L.39, Y.46, I.79, S.83, P.84, Q.116, Y.120, I.123, M.124, I.128 Ligands: OLC.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.39, A:Y.120, A:I.123, A:I.123, A:I.128 Hydrogen bonds: A:Q.116 OLC.4: 10 residues within 4Å: Chain A: I.147, I.150, I.151, P.153, I.154, M.157, C.204, L.207, L.208, L.211 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.147, A:I.147, A:I.150, A:I.151, A:P.153, A:M.157, A:L.211, A:L.211 Hydrogen bonds: A:M.157 OLC.7: 4 residues within 4Å: Chain A: A.43, Y.46, F.209 Ligands: OLC.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.209

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: E.197, M.200, H.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.197 GOL.6: 4 residues within 4Å: Chain A: A.43, G.47, W.49, L.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.49, A:L.50 GOL.10: 2 residues within 4Å: Chain A: E.70, T.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.70 GOL.11: 7 residues within 4Å: Chain A: A.33, F.34, F.37, L.148, T.149, F.152, I.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.37, A:T.149 GOL.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PG5.8: 6 residues within 4Å: Chain A: W.49, Y.52, F.53, D.56, K.68, K.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.68, A:K.68, A:K.72 PG5.9: 5 residues within 4Å: Chain A: P.84, F.85, N.110, V.113, K.114 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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