SMTL ID : 8b01.1

Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in a nanodisc

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

6 x OCT: N-OCTANE(Non-covalent)(Non-functional Binders)

OCT.1: 3 residues within 4Å: Chain A: S.30, W.33, L.34 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.33, A:W.33, A:L.34 OCT.7: 1 residues within 4Å: Chain B: L.32 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.32 OCT.8: 3 residues within 4Å: Chain B: I.87, Y.188 Ligands: HEX.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.87, B:Y.188 OCT.9: 3 residues within 4Å: Chain B: M.83, R.204, F.211 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.211 OCT.10: 1 residues within 4Å: Ligands: OCT.11 No protein-ligand interaction detected (PLIP) OCT.11: 4 residues within 4Å: Chain B: L.170, I.225, F.229 Ligands: OCT.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.170, B:I.225, B:F.229, B:F.229

2 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.2: 9 residues within 4Å: Chain A: I.12, L.17, A.20, W.41, L.45, H.52, T.118, L.119, W.125 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.17, A:A.20, A:W.41, A:L.45, A:W.125 PTY.14: 7 residues within 4Å: Chain A: L.22, C.23 Chain B: L.244, T.251, T.258, M.259, F.262 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.244, B:T.251, B:F.262, B:F.262, A:L.22 Hydrogen bonds: B:M.259

1 x TWT: DOCOSANE(Non-covalent)

TWT.3: 4 residues within 4Å: Chain A: P.16, A.20 Chain B: Q.267 Ligands: D10.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.20

2 x D10: DECANE(Non-covalent)

D10.4: 3 residues within 4Å: Chain A: W.27, W.41 Ligands: TWT.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.27, A:W.41 D10.13: 2 residues within 4Å: Chain B: A.182, M.186 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.182

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 6 residues within 4Å: Chain B: S.103, S.106, G.107, G.145, V.148, P.150 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.150 NA.6: 5 residues within 4Å: Chain B: G.325, T.326, G.366, T.369, M.372 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.369, B:T.369, B:T.369

1 x TRD: TRIDECANE(Non-covalent)

TRD.12: 2 residues within 4Å: Chain B: M.83, R.201 No protein-ligand interaction detected (PLIP)

1 x HEX: HEXANE(Non-covalent)

HEX.15: 3 residues within 4Å: Chain B: V.84, C.184 Ligands: OCT.8 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davies, J.S. et al., Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter. Nat Commun (2023)

Release Date

2023-03-15

Peptides

Putative TRAP-type C4-dicarboxylate transport system, small permease component: A
Putative TRAP-type C4-dicarboxylate transport system, large permease component: B
Megabody c7HopQ: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Putative TRAP-type C4-dicarboxylate transport system, small permease component

Putative TRAP-type C4-dicarboxylate transport system, large permease component

Megabody c7HopQ

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