SMTL ID : 8b17.1

DtpB-Nb132-AWA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ALA- TRP- ALA: ALA-TRP-ALA(Non-covalent)

ALA-TRP-ALA.1: 16 residues within 4Å: Chain A: R.27, Y.31, Y.64, K.123, Y.149, I.152, N.153, S.156, Y.282, Y.285, N.318, E.393, S.397, L.401, W.420, Q.424 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.31, A:Y.149, A:I.152, A:Y.285, A:L.401, A:W.420 Hydrogen bonds: A:Y.31, A:Y.64, A:N.153, A:Y.285, A:Y.285, A:N.318, A:E.393, A:Q.424 Water bridges: A:R.27 Salt bridges: A:R.27, A:K.123

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.2: 12 residues within 4Å: Chain A: L.162, V.165, D.168, R.169, S.308, I.309, N.310, S.313, F.314 Chain B: Y.31, F.98, N.111 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.162, A:V.165, A:F.314 Hydrogen bonds: A:V.165, A:D.168, A:R.169, A:R.169, A:N.310, B:Y.31, B:N.111, B:N.111 Salt bridges: A:R.169 Water bridges: B:F.98

1 x OCT: N-OCTANE(Non-covalent)

OCT.3: 2 residues within 4Å: Chain A: R.82, L.86 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.82, A:L.86

5 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 5 residues within 4Å: Chain A: L.361, T.362, M.368, W.369 Ligands: PG4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.362, A:T.362 PG4.6: 4 residues within 4Å: Chain A: M.368, L.463, L.466 Ligands: PG4.4 No protein-ligand interaction detected (PLIP) PG4.7: 3 residues within 4Å: Chain A: V.222, F.226 Ligands: PG4.9 No protein-ligand interaction detected (PLIP) PG4.8: 7 residues within 4Å: Chain A: I.69, L.77, K.213, Y.216, G.220, S.221, M.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.213, A:G.220 PG4.9: 3 residues within 4Å: Chain A: I.225, F.226 Ligands: PG4.7 No protein-ligand interaction detected (PLIP)

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5: 2 residues within 4Å: Chain A: N.456, K.460 No protein-ligand interaction detected (PLIP) 1PE.12: 8 residues within 4Å: Chain A: E.236, N.239, I.243, S.246, A.426, L.430, Y.433 Ligands: HEX.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.236, A:S.246, A:S.246

1 x D12: DODECANE(Non-covalent)

D12.10: 2 residues within 4Å: Chain A: M.209, L.215 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 3 residues within 4Å: Chain A: Q.12, R.14, F.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.14 GOL.14: 3 residues within 4Å: Chain A: W.369, F.370, A.371 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.369

1 x D10: DECANE(Non-covalent)

D10.13: 3 residues within 4Å: Chain A: K.104, D.106, L.107 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.104, A:K.104, A:D.106, A:L.107

2 x HEX: HEXANE(Non-functional Binders)

HEX.15: 1 residues within 4Å: Ligands: 1PE.12 No protein-ligand interaction detected (PLIP) HEX.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kotov, V. et al., Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition. Cell Rep (2023)

Release Date

2023-08-09

Peptides

Dipeptide and tripeptide permease B: A
Nanobody 132: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Dipeptide and tripeptide permease B

Nanobody 132

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