SMTL ID : 4ezd.1

Crystal Structure of the UT-B Urea Transporter from Bos Taurus Bound to Selenourea

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

6 x SEY: selenourea(Non-covalent)

SEY.1: 5 residues within 4Å: Chain A: L.127, Q.227, I.228, F.283, G.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.227, A:Q.227 SEY.2: 6 residues within 4Å: Chain A: Q.63, F.66, L.116, Y.119, F.171, F.296 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.63, A:Q.63 SEY.10: 5 residues within 4Å: Chain B: L.127, Q.227, I.228, F.283, G.333 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.227, B:Q.227 SEY.11: 6 residues within 4Å: Chain B: Q.63, F.66, L.116, Y.119, F.171, F.296 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63, B:Q.63 SEY.18: 7 residues within 4Å: Chain C: L.127, Q.227, I.228, G.230, F.283, G.333, T.334 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.227, C:Q.227, C:G.230 SEY.19: 6 residues within 4Å: Chain C: Q.63, F.66, L.116, Y.119, F.171, F.296 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.63, C:Q.63

8 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.3: 2 residues within 4Å: Chain A: Y.137, W.139 No protein-ligand interaction detected (PLIP) BGC.4: 4 residues within 4Å: Chain A: Y.137, F.138, W.139, W.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.139, A:W.140 BGC.12: 2 residues within 4Å: Chain B: S.375, R.376 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.376 BGC.13: 2 residues within 4Å: Chain B: Y.137, W.139 No protein-ligand interaction detected (PLIP) BGC.14: 4 residues within 4Å: Chain B: Y.137, F.138, W.139, W.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.139 BGC.20: 1 residues within 4Å: Chain C: W.301 No protein-ligand interaction detected (PLIP) BGC.21: 2 residues within 4Å: Chain C: T.208, D.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.208 BGC.22: 2 residues within 4Å: Chain C: Y.137, W.139 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.139

10 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.5: 4 residues within 4Å: Chain A: K.219, P.234, W.235, G.238 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.235, A:W.235 Hydrogen bonds: A:K.219 Salt bridges: A:K.219 BOG.6: 5 residues within 4Å: Chain A: L.212, S.213, A.214, L.215, L.217 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.217 Hydrogen bonds: A:A.214, A:L.215 BOG.7: 5 residues within 4Å: Chain A: K.134, W.140, F.192, F.193 Ligands: BOG.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.140, A:W.140, A:F.192, A:F.192, A:F.193 Hydrogen bonds: A:K.134 Salt bridges: A:K.134 BOG.15: 3 residues within 4Å: Chain B: W.209, L.267 Ligands: BOG.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.209, B:W.209 BOG.16: 8 residues within 4Å: Chain B: K.134, F.138, W.140, P.191, F.192, F.193 Chain C: S.268 Ligands: BOG.26 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.140, B:F.192, B:F.193 Hydrogen bonds: B:W.140 BOG.23: 6 residues within 4Å: Chain C: L.212, S.213, A.214, L.215, L.217, L.267 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.217, C:L.267 Hydrogen bonds: C:S.213, C:A.214, C:L.215 BOG.24: 5 residues within 4Å: Chain A: W.209, I.264, L.267 Chain C: F.192 Ligands: BOG.27 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.192, A:I.264 BOG.25: 6 residues within 4Å: Chain C: Y.137, F.138, W.139, W.140, L.142, F.143 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.142 Hydrogen bonds: C:Y.137, C:W.139 BOG.26: 4 residues within 4Å: Chain B: F.192 Chain C: W.209, L.267 Ligands: BOG.16 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.209 BOG.27: 7 residues within 4Å: Chain A: S.268 Chain C: K.134, F.138, W.140, F.192, F.193 Ligands: BOG.24 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.140, C:F.192, C:F.193 Hydrogen bonds: C:K.134, C:W.140 Salt bridges: C:K.134

3 x SPL: OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE(Non-covalent)

SPL.8: 14 residues within 4Å: Chain A: L.163, L.317, S.320, V.324, L.339, L.343, L.346 Chain C: V.162, M.177, S.180, M.181, M.325, L.330, W.335 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:V.162, C:M.177, C:W.335, C:W.335, A:L.163, A:L.317, A:L.339, A:L.343, A:L.346 Hydrogen bonds: A:S.320, A:S.320 SPL.9: 15 residues within 4Å: Chain A: F.155, V.162, M.177, S.180, M.181, S.184, M.325, L.330, W.335 Chain B: L.163, L.317, S.320, V.324, L.339, L.346 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.163, B:L.317, A:F.155, A:V.162, A:L.330, A:W.335, A:W.335 Hydrogen bonds: B:S.320, B:S.320, A:S.184 SPL.17: 16 residues within 4Å: Chain B: V.162, M.177, S.180, M.181, M.325, L.330, W.335, L.339 Chain C: L.163, W.166, L.317, S.320, V.324, L.339, L.343, L.346 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:L.163, C:W.166, C:L.317, C:L.339, C:L.343, C:L.346, B:V.162, B:M.177, B:L.330, B:W.335, B:W.335, B:L.339 Hydrogen bonds: C:S.320, C:S.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Levin, E.J. et al., Structure and permeation mechanism of a mammalian urea transporter. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-06-27

Peptides

Urea transporter 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Urea transporter 1

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