SMTL ID : 8blp.1

Human Urea Transporter UT-B/UT1 in Complex with Inhibitor UTBinh-14

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 22 residues within 4Å: Chain A: K.110, F.114, W.116, L.119, P.120, A.123, M.124, M.157, Y.158, A.161, P.167, F.168, F.169 Chain B: W.185, A.240, L.243, S.244, L.245, Y.292 Ligands: PTY.7, LMT.9, LMT.41 19 PLIP interactions: 12 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:W.116, A:L.119, A:P.120, A:A.123, A:Y.158, A:A.161, A:F.168, A:F.168, A:F.169, B:W.185, B:W.185, B:L.245, B:L.245, B:Y.292, B:Y.292, B:Y.292 Hydrogen bonds: A:K.110, A:F.168 Salt bridges: A:K.110 PTY.7: 11 residues within 4Å: Chain A: K.110, D.112, Y.113, F.114, W.115, W.116, L.118, L.119 Ligands: PTY.1, LMT.2, LMT.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.115, A:W.116, A:W.116, A:L.118, A:L.118, A:L.119, A:L.119 Hydrogen bonds: A:K.110, A:W.115, A:W.116 PTY.25: 22 residues within 4Å: Chain B: K.110, F.114, W.116, L.119, P.120, A.123, M.124, M.157, Y.158, A.161, P.167, F.168, F.169 Chain C: W.185, A.240, L.243, S.244, L.245, Y.292 Ligands: PTY.31, LMT.33, LMT.63 19 PLIP interactions: 12 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:W.116, B:L.119, B:P.120, B:A.123, B:Y.158, B:A.161, B:F.168, B:F.168, B:F.169, C:W.185, C:W.185, C:W.185, C:L.245, C:Y.292, C:Y.292, C:Y.292 Hydrogen bonds: B:K.110, B:F.168 Salt bridges: B:K.110 PTY.31: 11 residues within 4Å: Chain B: K.110, D.112, Y.113, F.114, W.115, W.116, L.118, L.119 Ligands: PTY.25, LMT.26, LMT.32 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.115, B:W.116, B:W.116, B:L.118, B:L.118, B:L.119, B:L.119 Hydrogen bonds: B:K.110, B:W.115, B:W.116 PTY.47: 22 residues within 4Å: Chain A: W.185, A.240, L.243, S.244, L.245, Y.292 Chain C: K.110, F.114, W.116, L.119, P.120, A.123, M.124, M.157, Y.158, A.161, P.167, F.168, F.169 Ligands: LMT.17, PTY.53, LMT.55 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:W.116, C:L.119, C:P.120, C:A.123, C:Y.158, C:A.161, C:F.168, C:F.168, C:F.169, A:W.185, A:L.245, A:Y.292, A:Y.292, A:Y.292 Hydrogen bonds: C:K.110, C:F.168 Salt bridges: C:K.110 PTY.53: 11 residues within 4Å: Chain C: K.110, D.112, Y.113, F.114, W.115, W.116, L.118, L.119 Ligands: PTY.47, LMT.48, LMT.54 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.115, C:W.116, C:W.116, C:L.118, C:L.118, C:L.119, C:L.119 Hydrogen bonds: C:K.110, C:W.115, C:W.116

51 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)(Non-functional Binders)

LMT.2: 7 residues within 4Å: Chain A: L.57, P.61, W.68, Y.113, W.115 Ligands: PTY.7, LMT.16 Ligand excluded by PLIP LMT.3: 6 residues within 4Å: Chain A: N.209, P.210, G.214, L.217, G.218 Ligands: LMT.5 Ligand excluded by PLIP LMT.4: 3 residues within 4Å: Chain A: L.188, L.193 Ligands: LMT.17 Ligand excluded by PLIP LMT.5: 4 residues within 4Å: Chain A: L.194, K.195 Ligands: LMT.3, LMT.14 Ligand excluded by PLIP LMT.6: 4 residues within 4Å: Chain A: V.58, N.209, W.211, I.215 Ligand excluded by PLIP LMT.8: 3 residues within 4Å: Chain A: W.116, L.119 Ligands: PTY.7 Ligand excluded by PLIP LMT.9: 3 residues within 4Å: Chain A: W.116 Ligands: PTY.1, LMT.24 Ligand excluded by PLIP LMT.10: 6 residues within 4Å: Chain A: L.76, M.77, L.79, L.80, M.126 Ligands: LMT.12 Ligand excluded by PLIP LMT.11: 4 residues within 4Å: Chain A: V.25, F.29, L.76, L.79 Ligand excluded by PLIP LMT.12: 2 residues within 4Å: Chain A: L.80 Ligands: LMT.10 Ligand excluded by PLIP LMT.13: 5 residues within 4Å: Chain A: L.6, L.51, G.218, L.221, L.222 Ligand excluded by PLIP LMT.14: 4 residues within 4Å: Chain A: P.225, C.228, L.229 Ligands: LMT.5 Ligand excluded by PLIP LMT.15: 8 residues within 4Å: Chain A: L.229, I.233, L.275, T.276, W.277, Q.278, H.280, R.345 Ligand excluded by PLIP LMT.16: 3 residues within 4Å: Chain A: L.57, Y.113 Ligands: LMT.2 Ligand excluded by PLIP LMT.17: 7 residues within 4Å: Chain A: W.185, S.186, L.188, L.243 Ligands: LMT.4, LMT.22, PTY.47 Ligand excluded by PLIP LMT.18: 1 residues within 4Å: Chain A: L.57 Ligand excluded by PLIP LMT.22: 2 residues within 4Å: Ligands: LMT.17, LMT.55 Ligand excluded by PLIP LMT.24: 2 residues within 4Å: Ligands: LMT.9, LMT.41 Ligand excluded by PLIP LMT.26: 7 residues within 4Å: Chain B: L.57, P.61, W.68, Y.113, W.115 Ligands: PTY.31, LMT.40 Ligand excluded by PLIP LMT.27: 6 residues within 4Å: Chain B: N.209, P.210, G.214, L.217, G.218 Ligands: LMT.29 Ligand excluded by PLIP LMT.28: 3 residues within 4Å: Chain B: L.188, L.193 Ligands: LMT.41 Ligand excluded by PLIP LMT.29: 4 residues within 4Å: Chain B: L.194, K.195 Ligands: LMT.27, LMT.38 Ligand excluded by PLIP LMT.30: 4 residues within 4Å: Chain B: V.58, N.209, W.211, I.215 Ligand excluded by PLIP LMT.32: 3 residues within 4Å: Chain B: W.116, L.119 Ligands: PTY.31 Ligand excluded by PLIP LMT.33: 3 residues within 4Å: Chain B: W.116 Ligands: PTY.25, LMT.46 Ligand excluded by PLIP LMT.34: 6 residues within 4Å: Chain B: L.76, M.77, L.79, L.80, M.126 Ligands: LMT.36 Ligand excluded by PLIP LMT.35: 4 residues within 4Å: Chain B: V.25, F.29, L.76, L.79 Ligand excluded by PLIP LMT.36: 2 residues within 4Å: Chain B: L.80 Ligands: LMT.34 Ligand excluded by PLIP LMT.37: 5 residues within 4Å: Chain B: L.6, L.51, G.218, L.221, L.222 Ligand excluded by PLIP LMT.38: 4 residues within 4Å: Chain B: P.225, C.228, L.229 Ligands: LMT.29 Ligand excluded by PLIP LMT.39: 7 residues within 4Å: Chain B: L.229, I.233, T.276, W.277, Q.278, H.280, R.345 Ligand excluded by PLIP LMT.40: 3 residues within 4Å: Chain B: L.57, Y.113 Ligands: LMT.26 Ligand excluded by PLIP LMT.41: 7 residues within 4Å: Chain B: W.185, S.186, L.188, L.243 Ligands: PTY.1, LMT.24, LMT.28 Ligand excluded by PLIP LMT.42: 1 residues within 4Å: Chain B: L.57 Ligand excluded by PLIP LMT.46: 2 residues within 4Å: Ligands: LMT.33, LMT.63 Ligand excluded by PLIP LMT.48: 7 residues within 4Å: Chain C: L.57, P.61, W.68, Y.113, W.115 Ligands: PTY.53, LMT.62 Ligand excluded by PLIP LMT.49: 6 residues within 4Å: Chain C: N.209, P.210, G.214, L.217, G.218 Ligands: LMT.51 Ligand excluded by PLIP LMT.50: 3 residues within 4Å: Chain C: L.188, L.193 Ligands: LMT.63 Ligand excluded by PLIP LMT.51: 4 residues within 4Å: Chain C: L.194, K.195 Ligands: LMT.49, LMT.60 Ligand excluded by PLIP LMT.52: 4 residues within 4Å: Chain C: V.58, N.209, W.211, I.215 Ligand excluded by PLIP LMT.54: 3 residues within 4Å: Chain C: W.116, L.119 Ligands: PTY.53 Ligand excluded by PLIP LMT.55: 3 residues within 4Å: Chain C: W.116 Ligands: LMT.22, PTY.47 Ligand excluded by PLIP LMT.56: 6 residues within 4Å: Chain C: L.76, M.77, L.79, L.80, M.126 Ligands: LMT.58 Ligand excluded by PLIP LMT.57: 4 residues within 4Å: Chain C: V.25, F.29, L.76, L.79 Ligand excluded by PLIP LMT.58: 2 residues within 4Å: Chain C: L.80 Ligands: LMT.56 Ligand excluded by PLIP LMT.59: 5 residues within 4Å: Chain C: L.6, L.51, G.218, L.221, L.222 Ligand excluded by PLIP LMT.60: 4 residues within 4Å: Chain C: P.225, C.228, L.229 Ligands: LMT.51 Ligand excluded by PLIP LMT.61: 8 residues within 4Å: Chain C: L.229, I.233, L.275, T.276, W.277, Q.278, H.280, R.345 Ligand excluded by PLIP LMT.62: 3 residues within 4Å: Chain C: L.57, Y.113 Ligands: LMT.48 Ligand excluded by PLIP LMT.63: 7 residues within 4Å: Chain C: W.185, S.186, L.188, L.243 Ligands: PTY.25, LMT.46, LMT.50 Ligand excluded by PLIP LMT.64: 1 residues within 4Å: Chain C: L.57 Ligand excluded by PLIP

6 x 5D3: 10-(4-ethylphenyl)sulfonyl-~{N}-(thiophen-2-ylmethyl)-5-thia-1,8,11,12-tetrazatricyclo[7.3.0.0^{2,6}]dodeca-2(6),3,7,9,11-pentaen-7-amine(Non-covalent)

5D3.19: 17 residues within 4Å: Chain A: L.103, V.106, F.107, F.151, Q.203, I.204, G.206, F.254, L.256, W.257, F.259, G.294, V.295, P.307, A.308, C.309, T.310 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.103, A:L.256, A:L.256, A:W.257, A:F.259, A:F.259, A:T.310 Hydrogen bonds: A:Q.203 pi-Stacking: A:F.107, A:F.107 5D3.20: 18 residues within 4Å: Chain A: Q.39, V.40, F.42, L.92, Y.93, Y.95, S.132, N.136, L.144, P.145, V.146, F.147, T.148, M.271, F.272, F.313, V.338, T.339 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.92, A:L.92, A:Y.93, A:Y.93, A:Y.95, A:N.136, A:V.146, A:V.146, A:F.147, A:F.313, A:V.338 pi-Stacking: A:F.42, A:F.272, A:F.272 5D3.43: 17 residues within 4Å: Chain B: L.103, V.106, F.107, F.151, Q.203, I.204, G.206, F.254, L.256, W.257, F.259, G.294, V.295, P.307, A.308, C.309, T.310 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.103, B:L.256, B:L.256, B:W.257, B:F.259, B:F.259, B:T.310 Hydrogen bonds: B:Q.203 pi-Stacking: B:F.107, B:F.107 5D3.44: 18 residues within 4Å: Chain B: Q.39, V.40, F.42, L.92, Y.93, Y.95, S.132, N.136, L.144, P.145, V.146, F.147, T.148, M.271, F.272, F.313, V.338, T.339 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.92, B:L.92, B:Y.93, B:Y.93, B:Y.95, B:N.136, B:V.146, B:V.146, B:F.147, B:F.313, B:V.338 pi-Stacking: B:F.42, B:F.272, B:F.272 5D3.65: 17 residues within 4Å: Chain C: L.103, V.106, F.107, F.151, Q.203, I.204, G.206, F.254, L.256, W.257, F.259, G.294, V.295, P.307, A.308, C.309, T.310 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.103, C:L.256, C:L.256, C:W.257, C:F.259, C:F.259, C:T.310 Hydrogen bonds: C:Q.203 pi-Stacking: C:F.107, C:F.107 5D3.66: 18 residues within 4Å: Chain C: Q.39, V.40, F.42, L.92, Y.93, Y.95, S.132, N.136, L.144, P.145, V.146, F.147, T.148, M.271, F.272, F.313, V.338, T.339 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.92, C:L.92, C:Y.93, C:Y.93, C:Y.95, C:N.136, C:V.146, C:V.146, C:F.147, C:F.313, C:V.338 pi-Stacking: C:F.42, C:F.272, C:F.272

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.21: 15 residues within 4Å: Chain A: W.277, Q.278, L.281, L.282, G.285, L.288, F.320, N.327, N.329 Chain C: M.77, L.80, L.81, A.123, T.127, I.130 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:L.80, C:L.81, C:I.130, A:W.277, A:L.281, A:L.282, A:L.288, A:F.320 Hydrogen bonds: A:Q.278, A:N.327 Y01.23: 15 residues within 4Å: Chain A: M.77, L.80, L.81, A.123, T.127, I.130 Chain B: W.277, Q.278, L.281, L.282, G.285, L.288, F.320, N.327, N.329 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.277, B:L.281, B:L.282, B:L.288, B:F.320, A:L.80, A:L.81, A:I.130 Hydrogen bonds: B:Q.278, B:N.327 Y01.45: 15 residues within 4Å: Chain B: M.77, L.80, L.81, A.123, T.127, I.130 Chain C: W.277, Q.278, L.281, L.282, G.285, L.288, F.320, N.327, N.329 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:L.80, B:L.81, B:I.130, C:W.277, C:L.281, C:L.282, C:L.288, C:F.320 Hydrogen bonds: C:Q.278, C:N.327

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chi, G. et al., Structural characterization of human urea transporters UT-A and UT-B and their inhibition. Sci Adv (2023)

Release Date

2023-10-04

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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