SMTL ID : 8omz.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 9 residues within 4Å: Chain A: A.32, S.73, F.74, E.242, H.246, T.287, Y.289, G.290, E.291 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.73, A:F.74, A:E.242, A:G.290, A:E.291, A:E.291 TRS.12: 10 residues within 4Å: Chain C: A.32, S.72, S.73, F.74, E.242, T.287, Y.289, G.290, E.291 Ligands: BNG.15 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.73, C:F.74, C:G.290, C:E.291, C:E.291

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

BNG.2: 10 residues within 4Å: Chain A: V.359, D.360, Y.361, N.362, L.367 Chain C: I.375, I.376, S.379, A.381 Ligands: DMU.11 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.361, C:I.375, C:I.376 Hydrogen bonds: A:V.359, A:D.360, A:D.360, A:Y.361, A:N.362, A:N.362 BNG.3: 10 residues within 4Å: Chain A: M.126, V.130, V.238, E.242, I.346, R.352, V.353, E.356 Chain B: Y.107 Ligands: 1PE.8 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.238, A:E.242, A:I.346, B:Y.107 Hydrogen bonds: A:E.356 BNG.4: 6 residues within 4Å: Chain A: V.171, S.174, V.175, P.185 Chain C: L.147, L.167 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.171, A:V.171, A:V.175, C:L.167 Hydrogen bonds: A:S.174, A:S.174 BNG.5: 8 residues within 4Å: Chain A: A.112, G.115, W.116, V.119, L.120, L.405, K.408 Chain B: T.57 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.119, A:L.120, A:L.405 BNG.6: 7 residues within 4Å: Chain A: I.376, A.381, K.382, V.383, L.403 Chain C: N.362 Ligands: BNG.13 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.362 Hydrophobic interactions: A:I.376, A:L.403 BNG.7: 2 residues within 4Å: Chain A: I.355, E.356 No protein-ligand interaction detected (PLIP) BNG.9: 6 residues within 4Å: Chain A: I.61, F.107, H.265, R.266, F.269 Ligands: DMU.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.61, A:F.269 Salt bridges: A:R.266 BNG.13: 11 residues within 4Å: Chain A: I.375, I.376, S.379, A.381 Chain C: V.359, D.360, Y.361, N.362, L.367 Ligands: BNG.6, DMU.18 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Y.361, C:L.367, A:I.375, A:I.376 Hydrogen bonds: C:V.359, C:Y.361, C:N.362 BNG.14: 7 residues within 4Å: Chain A: L.147, L.167 Chain C: V.171, S.174, V.175, P.185, L.341 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:V.175, C:L.341, A:L.147, A:L.147, A:L.167 Hydrogen bonds: C:S.174 BNG.15: 9 residues within 4Å: Chain C: V.238, E.242, S.349, R.352, V.353, E.356 Chain D: Y.107 Ligands: TRS.12, 1PE.16 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:E.242 Hydrogen bonds: C:S.349, C:R.352, C:R.352, C:E.356 BNG.17: 6 residues within 4Å: Chain C: A.112, G.115, W.116, V.119, L.405 Chain D: T.57 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.405 Hydrogen bonds: C:A.112, C:G.115

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

1PE.8: 6 residues within 4Å: Chain A: V.249, I.253, G.290, G.294 Chain B: E.114 Ligands: BNG.3 No protein-ligand interaction detected (PLIP) 1PE.16: 6 residues within 4Å: Chain C: G.245, H.246, V.249, I.253 Chain D: S.108 Ligands: BNG.15 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.108, C:H.246

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

DMU.10: 6 residues within 4Å: Chain A: R.12, F.60, K.63, G.64, G.308 Ligands: BNG.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.60 DMU.11: 15 residues within 4Å: Chain A: L.354, I.355, K.358, V.359, Y.361, S.371, L.374 Chain B: D.66 Chain C: S.371, L.374, I.375, V.378, S.379 Ligands: BNG.2, DMU.18 10 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:L.354, A:L.374, C:L.374, C:I.375 Hydrogen bonds: A:I.355, A:K.358, A:V.359, A:V.359, B:D.66 Salt bridges: A:K.358 DMU.18: 16 residues within 4Å: Chain A: L.374, I.375, V.378, S.379 Chain C: L.354, I.355, K.358, V.359, Y.361, T.370, L.374 Chain D: Y.64, D.66, K.69 Ligands: DMU.11, BNG.13 10 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A, 5 interactions with chain C Hydrogen bonds: D:Y.64, D:D.66, D:K.69, C:L.354, C:V.359 Hydrophobic interactions: A:L.374, A:I.375, C:T.370, C:L.374 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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