SMTL ID : 3k3g.1

Crystal Structure of the Urea Transporter from Desulfovibrio Vulgaris Bound to 1,3-dimethylurea

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-trimer

Ligands

27 x AU: GOLD ION(Non-covalent)(Covalent)

AU.1: 2 residues within 4Å: Chain A: Q.27, F.30 Ligand excluded by PLIP AU.2: 5 residues within 4Å: Chain A: C.22, T.34, L.38 Ligands: AU.3, AU.4 Ligand excluded by PLIP AU.3: 5 residues within 4Å: Chain A: C.18, C.22 Ligands: AU.2, AU.4, AU.5 Ligand excluded by PLIP AU.4: 5 residues within 4Å: Chain A: C.18, D.19 Ligands: AU.2, AU.3, AU.5 Ligand excluded by PLIP AU.5: 3 residues within 4Å: Chain A: C.18 Ligands: AU.3, AU.4 Ligand excluded by PLIP AU.6: 5 residues within 4Å: Chain A: T.50, V.53, C.54, L.103 Ligands: AU.7 Ligand excluded by PLIP AU.7: 6 residues within 4Å: Chain A: T.50, C.54, P.93, M.102, L.103 Ligands: AU.6 Ligand excluded by PLIP AU.8: 2 residues within 4Å: Chain A: C.227 Ligands: AU.9 Ligand excluded by PLIP AU.9: 2 residues within 4Å: Chain A: C.227 Ligands: AU.8 Ligand excluded by PLIP AU.12: 2 residues within 4Å: Chain B: Q.27, F.30 Ligand excluded by PLIP AU.13: 5 residues within 4Å: Chain B: C.22, T.34, L.38 Ligands: AU.14, AU.15 Ligand excluded by PLIP AU.14: 5 residues within 4Å: Chain B: C.18, C.22 Ligands: AU.13, AU.15, AU.16 Ligand excluded by PLIP AU.15: 5 residues within 4Å: Chain B: C.18, D.19 Ligands: AU.13, AU.14, AU.16 Ligand excluded by PLIP AU.16: 3 residues within 4Å: Chain B: C.18 Ligands: AU.14, AU.15 Ligand excluded by PLIP AU.17: 5 residues within 4Å: Chain B: T.50, V.53, C.54, L.103 Ligands: AU.18 Ligand excluded by PLIP AU.18: 6 residues within 4Å: Chain B: T.50, C.54, P.93, M.102, L.103 Ligands: AU.17 Ligand excluded by PLIP AU.19: 2 residues within 4Å: Chain B: C.227 Ligands: AU.20 Ligand excluded by PLIP AU.20: 2 residues within 4Å: Chain B: C.227 Ligands: AU.19 Ligand excluded by PLIP AU.23: 2 residues within 4Å: Chain C: Q.27, F.30 Ligand excluded by PLIP AU.24: 5 residues within 4Å: Chain C: C.22, T.34, L.38 Ligands: AU.25, AU.26 Ligand excluded by PLIP AU.25: 5 residues within 4Å: Chain C: C.18, C.22 Ligands: AU.24, AU.26, AU.27 Ligand excluded by PLIP AU.26: 5 residues within 4Å: Chain C: C.18, D.19 Ligands: AU.24, AU.25, AU.27 Ligand excluded by PLIP AU.27: 3 residues within 4Å: Chain C: C.18 Ligands: AU.25, AU.26 Ligand excluded by PLIP AU.28: 5 residues within 4Å: Chain C: T.50, V.53, C.54, L.103 Ligands: AU.29 Ligand excluded by PLIP AU.29: 6 residues within 4Å: Chain C: T.50, C.54, P.93, M.102, L.103 Ligands: AU.28 Ligand excluded by PLIP AU.30: 2 residues within 4Å: Chain C: C.227 Ligands: AU.31 Ligand excluded by PLIP AU.31: 2 residues within 4Å: Chain C: C.227 Ligands: AU.30 Ligand excluded by PLIP

6 x MMU: 1,3-dimethylurea(Non-covalent)

MMU.10: 6 residues within 4Å: Chain A: E.190, V.191, F.193, F.246, L.296, T.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.190, A:E.190 MMU.11: 7 residues within 4Å: Chain A: Q.27, V.28, F.30, L.80, F.83, L.132, T.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.27, A:Q.27 Water bridges: A:L.132 MMU.21: 6 residues within 4Å: Chain B: E.190, V.191, F.193, F.246, L.296, T.297 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.190, B:E.190 MMU.22: 7 residues within 4Å: Chain B: Q.27, V.28, F.30, L.80, F.83, L.132, T.133 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.27, B:Q.27 Water bridges: B:L.132 MMU.32: 6 residues within 4Å: Chain C: E.190, V.191, F.193, F.246, L.296, T.297 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.190, C:E.190 MMU.33: 7 residues within 4Å: Chain C: Q.27, V.28, F.30, L.80, F.83, L.132, T.133 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.27, C:Q.27 Water bridges: C:L.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Levin, E.J. et al., Crystal structure of a bacterial homologue of the kidney urea transporter. Nature (2009)

Release Date

2009-11-17

Peptides

Urea transporter: 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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Urea transporter

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