SMTL ID : 8oo1.1

Wide inward-open liganded UraA in complex with a conformation-selective synthetic nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

hetero-2-2-mer

Ligands

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

1PE.1: 8 residues within 4Å: Chain A: V.249, N.252, I.253, G.290, I.293, G.294 Chain B: E.114 Ligands: BNG.2 No protein-ligand interaction detected (PLIP) 1PE.11: 5 residues within 4Å: Chain C: V.249, G.294 Chain D: S.108, E.114 Ligands: BNG.6 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.108

5 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.2: 9 residues within 4Å: Chain A: M.126, V.130, V.238, E.242, R.352, V.353, E.356 Chain B: Y.107 Ligands: 1PE.1 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.107, A:V.130, A:E.242 Hydrogen bonds: A:R.352, A:E.356 BNG.3: 8 residues within 4Å: Chain A: V.171, S.174, V.175, A.182, P.185, I.186 Chain C: L.147, L.167 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.147, C:L.147, C:L.167, A:V.175 Hydrogen bonds: A:S.174 BNG.6: 12 residues within 4Å: Chain C: F.74, M.126, V.130, V.238, E.242, S.349, R.352, V.353, E.356 Chain D: Y.107 Ligands: URA.9, 1PE.11 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.74, C:V.238, C:E.242, D:Y.107 Hydrogen bonds: C:S.349, C:R.352, C:E.356 BNG.7: 8 residues within 4Å: Chain A: L.147, L.167, L.340 Chain C: V.171, S.174, V.175, L.341, V.345 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:L.147, A:L.167, C:V.171, C:V.175 Hydrogen bonds: C:S.174 BNG.8: 7 residues within 4Å: Chain C: A.112, G.115, W.116, V.119, L.405, L.409 Chain D: T.57 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.116, C:V.119, C:L.405, C:L.409 Hydrogen bonds: C:A.112

2 x URA: URACIL(Non-covalent)

URA.4: 10 residues within 4Å: Chain A: A.32, S.72, S.73, F.74, E.242, H.246, T.287, Y.289, G.290, E.291 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.74, A:Y.289 Hydrogen bonds: A:F.74, A:E.242, A:G.290, A:E.291, A:E.291 URA.9: 10 residues within 4Å: Chain C: S.72, S.73, F.74, E.242, H.246, T.287, Y.289, G.290, E.291 Ligands: BNG.6 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.74 Hydrogen bonds: C:F.74, C:E.242, C:G.290, C:E.291 pi-Stacking: C:Y.289

2 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.5: 12 residues within 4Å: Chain A: L.354, I.355, K.358, Y.361, S.371, L.374 Chain B: D.66, K.69 Chain C: I.375, V.378, S.379 Ligands: DMU.10 11 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:L.354, A:L.354, A:Y.361, A:L.374, C:I.375, C:V.378 Hydrogen bonds: A:I.355, A:K.358, B:D.66, B:K.69 Salt bridges: A:K.358 DMU.10: 13 residues within 4Å: Chain A: I.375, V.378, S.379 Chain C: L.354, I.355, K.358, V.359, Y.361, T.370, S.371, L.374 Chain D: D.66 Ligands: DMU.5 10 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: C:L.354, C:L.354, C:I.355, C:Y.361, C:L.374, A:I.375 Hydrogen bonds: C:V.359, D:D.66, D:K.69 Salt bridges: C:K.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuhn, B.T. et al., Interdomain-linkers control conformational transitions in the SLC23 elevator transporter UraA. Nat Commun (2024)

Release Date

2024-04-10

Peptides

Uracil permease: AC
Sy45: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Membrane

We predict this structure to be a membrane protein.
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Uracil permease

Sy45

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