SMTL ID : 6xq6.1

Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

14 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: G.1, A.2, A.4, I.77, R.79, N.93 Chain B: A.41 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.4, A:I.77 Hydrogen bonds: A:A.2, A:N.93, A:N.93 Salt bridges: A:R.79 ACT.2: 5 residues within 4Å: Chain A: A.2, R.79 Chain B: K.33, W.42, V.44 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.33, B:V.44 Salt bridges: B:K.33, A:R.79 Water bridges: A:A.2 ACT.3: 7 residues within 4Å: Chain A: Q.5, K.20, K.91, S.92, N.93, Y.94 Chain D: K.155 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:K.155 Salt bridges: D:K.155, A:K.20 Hydrogen bonds: A:K.91, A:N.93 ACT.4: 6 residues within 4Å: Chain A: E.156, Q.157, T.158 Chain D: N.6, R.95, R.97 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:E.156, A:T.158, A:T.158, D:N.6 Hydrophobic interactions: D:R.95 Water bridges: D:R.97, D:R.97, D:R.97 Salt bridges: D:R.97 ACT.8: 7 residues within 4Å: Chain A: A.41 Chain B: G.1, A.2, A.4, I.77, R.79, N.93 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.4, B:I.77 Hydrogen bonds: B:A.2, B:N.93, B:N.93 Salt bridges: B:R.79 ACT.9: 5 residues within 4Å: Chain A: K.33, W.42, V.44 Chain B: A.2, R.79 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.33, A:V.44 Salt bridges: A:K.33, B:R.79 Water bridges: B:A.2 ACT.10: 7 residues within 4Å: Chain B: Q.5, K.20, K.91, S.92, N.93, Y.94 Chain C: K.155 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.91, B:N.93 Salt bridges: B:K.20, C:K.155 Hydrophobic interactions: C:K.155 ACT.11: 6 residues within 4Å: Chain B: E.156, Q.157, T.158 Chain C: N.6, R.95, R.97 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:E.156, B:T.158, B:T.158, C:N.6 Hydrophobic interactions: C:R.95 Water bridges: C:R.97, C:R.97, C:R.97 Salt bridges: C:R.97 ACT.15: 7 residues within 4Å: Chain C: G.1, A.2, A.4, I.77, R.79, N.93 Chain D: A.41 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.4, C:I.77 Hydrogen bonds: C:A.2, C:N.93 Salt bridges: C:R.79 ACT.16: 5 residues within 4Å: Chain C: A.2, R.79 Chain D: K.33, W.42, V.44 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Water bridges: C:A.2 Salt bridges: C:R.79, D:K.33 Hydrophobic interactions: D:K.33, D:V.44 ACT.17: 7 residues within 4Å: Chain B: K.155 Chain C: Q.5, K.20, K.91, S.92, N.93, Y.94 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Salt bridges: B:K.155, C:K.20 Hydrogen bonds: C:N.93, C:N.93 ACT.20: 7 residues within 4Å: Chain C: A.41 Chain D: G.1, A.2, A.4, I.77, R.79, N.93 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.4, D:I.77 Hydrogen bonds: D:A.2, D:N.93 Salt bridges: D:R.79 ACT.21: 5 residues within 4Å: Chain C: K.33, W.42, V.44 Chain D: A.2, R.79 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:K.33, C:V.44 Salt bridges: C:K.33, D:R.79 Water bridges: D:A.2 ACT.22: 7 residues within 4Å: Chain A: K.155 Chain D: Q.5, K.20, K.91, S.92, N.93, Y.94 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.93, D:N.93 Salt bridges: D:K.20, A:K.155

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: T.39, E.40 Chain C: R.159, R.160 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: T.39, E.40 Chain D: R.159, R.160 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: R.159, R.160 Chain C: T.39, E.40 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain B: R.159, R.160 Chain D: T.39, E.40 Ligand excluded by PLIP

6 x V6P: 3-phenoxyphenol(Non-covalent)

V6P.6: 4 residues within 4Å: Chain A: D.54, R.58, F.66, P.68 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.66, A:P.68 pi-Cation interactions: A:R.58 V6P.7: 6 residues within 4Å: Chain A: R.29, L.30, E.31, Q.81, A.82, M.83 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.29, A:R.29, A:Q.81 V6P.13: 4 residues within 4Å: Chain B: D.54, R.58, F.66, P.68 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.66, B:P.68 pi-Cation interactions: B:R.58 V6P.14: 6 residues within 4Å: Chain B: R.29, L.30, E.31, Q.81, A.82, M.83 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.29, B:R.29, B:Q.81 V6P.19: 6 residues within 4Å: Chain C: R.29, L.30, E.31, Q.81, A.82, M.83 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.29, C:R.29, C:Q.81 V6P.24: 6 residues within 4Å: Chain D: R.29, L.30, E.31, Q.81, A.82, M.83 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:R.29, D:R.29, D:Q.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kozlyuk, N. et al., A fragment-based approach to discovery of Receptor for Advanced Glycation End products inhibitors. Proteins (2021)

Release Date

2021-07-14

Peptides

Advanced glycosylation end product-specific receptor: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Advanced glycosylation end product-specific receptor

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