SMTL ID : 8j5t.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 21 residues within 4Å: Chain D: R.147, E.154, L.155, S.156, G.157, G.158, E.159, A.184, Y.359, V.374, A.376, S.396, G.397, S.398, G.399, K.400, S.401, T.402, Q.445, H.558 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:R.147, D:R.147, D:S.156, D:S.156, D:G.157, D:G.158, D:E.159, D:G.397, D:G.397, D:S.398, D:G.399, D:G.399, D:K.400, D:S.401, D:T.402, D:T.402 Salt bridges: D:K.400, D:K.400, D:H.558 pi-Stacking: D:Y.359, D:Y.359 ATP.3: 21 residues within 4Å: Chain D: F.14, T.16, A.23, E.42, S.43, G.44, S.45, G.46, K.47, S.48, A.49, Y.61, Q.96, H.213, R.495, E.499, F.500, S.501, G.503, Q.504 Ligands: MG.4 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:G.44, D:S.45, D:G.46, D:K.47, D:S.48, D:A.49, D:Y.61, D:Y.61, D:Q.96, D:R.495, D:R.495, D:G.503, D:Q.504 Salt bridges: D:K.47, D:K.47, D:H.213 pi-Stacking: D:F.14, D:F.14

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain D: S.401, Q.445, D.524 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.401 MG.4: 4 residues within 4Å: Chain D: S.48, Q.96, S.501 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.48

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

SF4.5: 11 residues within 4Å: Chain D: M.248, P.249, C.286, F.288, A.289, C.292, 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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