SMTL ID : 8j5s.1

Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the pre-catalytic intermediate state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: Endogenous oligopeptide(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 16 residues within 4Å: Chain A: N.110, N.111, A.112, S.193, N.230, S.338, Y.340, Y.441, F.475, F.489, G.490, W.491, V.492, D.494, S.499, Q.503 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.112, A:Y.340, A:F.475, A:W.491 Hydrogen bonds: A:N.110, A:A.112, A:N.230, A:S.338, A:G.490, A:G.490, A:V.492, A:V.492, A:S.499, A:S.499, A:Q.503, A:Q.503

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 13 residues within 4Å: Chain D: Y.359, V.374, A.376, E.395, S.396, G.397, S.398, G.399, K.400, S.401, T.402, Q.445 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.397, D:S.398, D:G.399, D:K.400, D:K.400, D:K.400, D:S.401, D:T.402, D:T.402, D:Q.445, D:Q.445 pi-Stacking: D:Y.359, D:Y.359 ANP.4: 16 residues within 4Å: Chain D: F.14, T.16, V.21, A.23, E.42, S.43, G.44, S.45, G.46, K.47, S.48, A.49, Y.61, Q.96, L.279 Ligands: MG.5 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.43, D:G.44, D:S.45, D:G.46, D:K.47, D:K.47, D:K.47, D:S.48, D:A.49, D:Y.61, D:Y.61, D:Q.96, D:S.278 pi-Stacking: D:F.14, D:F.14

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain D: S.401, Q.445 Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain D: S.48, Q.96 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.48

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.6: 9 residues within 4Å: Chain D: C.286, A.289, C.292, L.294, C.299, P.304, C.317, I.318, R.319 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.286, D:C.292, D:C.299, D:C.317

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X. et al., An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-04-03

Peptides

Uncharacterized protein Rv1280c: A
Putative peptide transport permease protein Rv1283c: B
Putative peptide transport permease protein Rv1282c: C
Uncharacterized ABC transporter ATP-binding protein Rv1281c: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Uncharacterized protein Rv1280c

Putative peptide transport permease protein Rv1283c

Putative peptide transport permease protein Rv1282c

Uncharacterized ABC transporter ATP-binding protein Rv1281c

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