SMTL ID : 3tij.1

Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-trimer

Ligands

3 x URI: URIDINE(Non-covalent)

URI.1: 12 residues within 4Å: Chain A: Q.160, A.191, V.194, Y.198, L.265, N.337, E.338, F.339, F.372, N.374, S.377, I.380 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.194, A:L.265, A:F.372 Hydrogen bonds: A:Q.160, A:Y.198, A:Y.198, A:F.372, A:N.374 Water bridges: A:T.161, A:E.162 URI.8: 12 residues within 4Å: Chain B: Q.160, A.191, V.194, Y.198, L.265, N.337, E.338, F.339, F.372, N.374, S.377, I.380 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.194, B:L.265, B:F.372 Hydrogen bonds: B:Q.160, B:Y.198, B:Y.198, B:F.372, B:N.374 Water bridges: B:T.161, B:E.162 URI.15: 12 residues within 4Å: Chain C: Q.160, A.191, V.194, Y.198, L.265, N.337, E.338, F.339, F.372, N.374, S.377, I.380 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.194, C:L.265, C:F.372 Hydrogen bonds: C:Q.160, C:Y.198, C:Y.198, C:F.372, C:N.374 Water bridges: C:T.161, C:E.162

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

DMU.2: 10 residues within 4Å: Chain A: L.301, V.335, L.375, I.378, A.397 Chain C: A.249, N.250, V.251, I.252 Ligands: DMU.4 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.301, A:V.335, A:L.375, C:V.251, C:I.252 Water bridges: A:L.375, A:V.401, C:D.253 Hydrogen bonds: C:N.250 DMU.4: 5 residues within 4Å: Chain A: F.276, L.279, I.283 Chain C: I.252 Ligands: DMU.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.276, A:L.279, A:I.283, C:I.252 DMU.5: 2 residues within 4Å: Chain A: I.156, L.195 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.195 DMU.6: 1 residues within 4Å: Chain A: I.405 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.405 DMU.7: 2 residues within 4Å: Chain A: L.48, F.213 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.48 DMU.9: 10 residues within 4Å: Chain A: A.249, N.250, V.251, I.252 Chain B: L.301, V.335, L.375, I.378, A.397 Ligands: DMU.11 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.251, A:I.252, B:L.301, B:V.335, B:L.375 Hydrogen bonds: A:N.250 Water bridges: A:D.253, B:L.375, B:V.401 DMU.11: 5 residues within 4Å: Chain A: I.252 Chain B: F.276, L.279, I.283 Ligands: DMU.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.276, B:L.279, B:I.283, A:I.252 DMU.12: 2 residues within 4Å: Chain B: I.156, L.195 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.195 DMU.13: 1 residues within 4Å: Chain B: I.405 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.405 DMU.14: 2 residues within 4Å: Chain B: L.48, F.213 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.48 DMU.16: 10 residues within 4Å: Chain B: A.249, N.250, V.251, I.252 Chain C: L.301, V.335, L.375, I.378, A.397 Ligands: DMU.18 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:V.251, B:I.252, C:L.301, C:V.335, C:L.375 Hydrogen bonds: B:N.250 Water bridges: B:D.253, C:L.375, C:V.401 DMU.18: 5 residues within 4Å: Chain B: I.252 Chain C: F.276, L.279, I.283 Ligands: DMU.16 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.276, C:L.279, C:I.283, B:I.252 DMU.19: 2 residues within 4Å: Chain C: I.156, L.195 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.195 DMU.20: 1 residues within 4Å: Chain C: I.405 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.405 DMU.21: 2 residues within 4Å: Chain C: L.48, F.213 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.48

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

NA.3: 5 residues within 4Å: Chain A: N.155, V.158, G.159, S.189, I.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.155 NA.10: 5 residues within 4Å: Chain B: N.155, V.158, G.159, S.189, I.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.158 NA.17: 5 residues within 4Å: Chain C: N.155, V.158, G.159, S.189, I.190 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, Z.L. et al., Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4A. Nature (2012)

Release Date

2012-03-07

Peptides

NupC family protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
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NupC family protein

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