SMTL ID : 6xq5.1

Receptor for Advanced Glycation End Products VC1 domain in complex with Fragment 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.4, A:I.77 Hydrogen bonds: A:A.2, A:N.93, A:N.93 Water bridges: A:G.1, A:R.79, A:R.79 Salt bridges: A:R.79 ACT.2: 6 residues within 4Å: Chain A: A.2, R.79 Chain B: K.33, W.42, V.44 Ligands: V6M.6 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.2 Salt bridges: A:R.79, B:K.33 Hydrophobic interactions: B:K.33, B:V.44 ACT.3: 7 residues within 4Å: Chain A: Q.5, K.20, K.91, S.92, N.93, Y.94 Chain D: K.155 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:K.20 Hydrogen bonds: A:K.91, A:N.93 Salt bridges: A:K.20, D:K.155 Water bridges: D:K.155 ACT.4: 6 residues within 4Å: Chain A: E.156, Q.157, T.158 Chain D: A.4, R.95, R.97 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:A.4, D:R.95 Water bridges: D:R.97 Salt bridges: D:R.97 Hydrogen bonds: A:E.156, A:T.158, A:T.158 ACT.7: 7 residues within 4Å: Chain A: A.41 Chain B: G.1, A.2, A.4, I.77, R.79, N.93 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.4, B:I.77 Hydrogen bonds: B:A.2, B:N.93, B:N.93 Water bridges: B:G.1, B:R.79, B:R.79 Salt bridges: B:R.79 ACT.8: 6 residues within 4Å: Chain A: K.33, W.42, V.44 Chain B: A.2, R.79 Ligands: V6M.12 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 Hydrogen bonds: B:A.2 ACT.9: 7 residues within 4Å: Chain B: Q.5, K.20, K.91, S.92, N.93, Y.94 Chain C: K.155 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:K.20 Hydrogen bonds: B:K.91, B:N.93 Salt bridges: B:K.20, C:K.155 Water bridges: C:K.155 ACT.10: 6 residues within 4Å: Chain B: E.156, Q.157, T.158 Chain C: A.4, R.95, R.97 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:A.4, C:R.95 Water bridges: C:R.97 Salt bridges: C:R.97 Hydrogen bonds: B:E.156, B:T.158, B:T.158 ACT.13: 7 residues within 4Å: Chain C: G.1, A.2, A.4, I.77, R.79, N.93 Chain D: A.41 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.4, C:I.77 Hydrogen bonds: C:A.2, C:N.93 Water bridges: C:G.1, C:R.79, C:R.79 Salt bridges: C:R.79 ACT.14: 6 residues within 4Å: Chain C: A.2, R.79 Chain D: K.33, W.42, V.44 Ligands: V6M.17 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D Water bridges: C:A.2, D:W.42 Salt bridges: C:R.79, D:K.33 Hydrophobic interactions: D:K.33, D:W.42, D:V.44 ACT.15: 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: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.93, C:N.93 Salt bridges: C:K.20, B:K.155 ACT.18: 7 residues within 4Å: Chain C: A.41 Chain D: G.1, A.2, A.4, I.77, R.79, N.93 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.4, D:I.77 Hydrogen bonds: D:A.2, D:N.93 Water bridges: D:G.1, D:R.79, D:R.79 Salt bridges: D:R.79 ACT.19: 6 residues within 4Å: Chain C: K.33, W.42, V.44 Chain D: A.2, R.79 Ligands: V6M.22 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Water bridges: D:A.2, C:W.42 Salt bridges: D:R.79, C:K.33 Hydrophobic interactions: C:K.33, C:W.42, C:V.44 ACT.20: 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.11: 4 residues within 4Å: Chain B: T.39, E.40 Chain D: R.159, R.160 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: R.159, R.160 Chain C: T.39, E.40 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: R.159, R.160 Chain D: T.39, E.40 Ligand excluded by PLIP

4 x V6M: 7-methyl-3-phenyl-1H-indole-2-carboxylic acid(Non-covalent)

V6M.6: 11 residues within 4Å: Chain A: A.2, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Ligands: ACT.2, V6M.12 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.2, A:E.31, A:K.33, A:K.33, A:Q.81, A:K.91, A:K.91, A:N.93 Salt bridges: A:K.33, A:K.91, B:K.33 pi-Cation interactions: A:R.79, A:K.91 V6M.12: 11 residues within 4Å: Chain B: A.2, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Ligands: V6M.6, ACT.8 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.2, B:E.31, B:K.33, B:K.33, B:Q.81, B:K.91, B:K.91, B:N.93 Salt bridges: B:K.33, B:K.91, A:K.33 pi-Cation interactions: B:R.79, B:K.91 V6M.17: 11 residues within 4Å: Chain C: A.2, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Ligands: ACT.14, V6M.22 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:A.2, C:E.31, C:K.33, C:Q.81, C:K.91, C:K.91, C:N.93 Salt bridges: C:K.33, C:K.91, D:K.33 pi-Cation interactions: C:R.79, C:K.91 V6M.22: 11 residues within 4Å: Chain D: A.2, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Ligands: V6M.17, ACT.19 12 PLIP interactions: 1 interactions with chain C, 11 interactions with chain D Salt bridges: C:K.33, D:K.33, D:K.91 Hydrophobic interactions: D:A.2, D:E.31, D:K.33, D:Q.81, D:K.91, D:K.91, D:N.93 pi-Cation interactions: D:R.79, D:K.91

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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