SMTL ID : 6xq8.1

Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-tetramer

Ligands

12 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 8 PLIP interactions: 8 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: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.5 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.33, B:V.44 Water bridges: B:K.33, B:K.33, A:A.2 Salt bridges: B:K.33, A:R.79 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: 4 interactions with chain A, 1 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 ACT.4: 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 ACT.8: 7 residues within 4Å: Chain A: A.41 Chain B: G.1, A.2, A.4, I.77, R.79, N.93 8 PLIP interactions: 8 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:R.79, B:R.79 Salt bridges: B:R.79 ACT.9: 6 residues within 4Å: Chain A: K.33, W.42, V.44 Chain B: A.2, R.79 Ligands: V6M.12 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.33, A:V.44 Water bridges: A:K.33, A:K.33, B:A.2 Salt bridges: A:K.33, B:R.79 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: 4 interactions with chain B, 1 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 ACT.11: 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.15: 7 residues within 4Å: Chain C: G.1, A.2, A.4, I.77, R.79, N.93 Chain D: A.41 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.4, C:I.77 Hydrogen bonds: C:A.2, C:N.93 Water bridges: C:R.79, C:R.79 Salt bridges: C:R.79 ACT.16: 6 residues within 4Å: Chain C: A.2, R.79 Chain D: K.33, W.42, V.44 Ligands: V6M.19 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D Water bridges: C:A.2, D:K.33, D:W.42 Salt bridges: C:R.79, D:K.33 Hydrophobic interactions: D:K.33, D:V.44 ACT.21: 7 residues within 4Å: Chain C: A.41 Chain D: G.1, A.2, A.4, I.77, R.79, N.93 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.4, D:I.77 Hydrogen bonds: D:A.2, D:N.93 Water bridges: D:R.79, D:R.79 Salt bridges: D:R.79 ACT.22: 6 residues within 4Å: Chain C: K.33, W.42, V.44 Chain D: A.2, R.79 Ligands: V6M.25 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:K.33, C:V.44 Water bridges: C:K.33, C:W.42, D:A.2 Salt bridges: C:K.33, D:R.79

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

V6M.5: 12 residues within 4Å: Chain A: A.2, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Chain B: K.33 Ligands: ACT.2, V6M.12 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.2, A:E.31, A:K.33, A:Q.81, A:K.91, A:K.91, A:N.93 Hydrogen bonds: A:K.91 Salt bridges: A:K.33, A:K.91, B:K.33 pi-Cation interactions: A:K.33, A:R.79, A:K.91 Water bridges: B:K.33 V6M.12: 12 residues within 4Å: Chain A: K.33 Chain B: A.2, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Ligands: V6M.5, ACT.9 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.2, B:E.31, B:K.33, B:Q.81, B:K.91, B:K.91, B:N.93 Hydrogen bonds: B:K.91 Salt bridges: B:K.33, B:K.91, A:K.33 pi-Cation interactions: B:K.33, B:R.79, B:K.91 Water bridges: A:K.33 V6M.19: 12 residues within 4Å: Chain C: A.2, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Chain D: K.33 Ligands: ACT.16, V6M.25 14 PLIP interactions: 2 interactions with chain D, 12 interactions with chain C Water bridges: D:K.33 Salt bridges: D:K.33, C:K.33 Hydrophobic interactions: C:A.2, C:E.31, C:K.33, C:Q.81, C:K.91, C:K.91, C:N.93 pi-Cation interactions: C:K.33, C:R.79, C:K.91, C:K.91 V6M.25: 12 residues within 4Å: Chain C: K.33 Chain D: A.2, E.31, K.33, R.79, C.80, Q.81, K.91, S.92, N.93 Ligands: V6M.19, ACT.22 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.2, D:E.31, D:K.33, D:Q.81, D:K.91, D:K.91, D:N.93 Salt bridges: D:K.33, C:K.33 pi-Cation interactions: D:K.33, D:R.79, D:K.91, D:K.91 Water bridges: C:K.33

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

V6P.6: 7 residues within 4Å: Chain A: Q.28, R.29, L.30, E.31, S.46, P.47, Q.81 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.31, A:Q.81 Hydrogen bonds: A:E.31, A:E.31 V6P.7: 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:P.68 Hydrogen bonds: A:F.66 pi-Cation interactions: A:R.58 V6P.13: 7 residues within 4Å: Chain B: Q.28, R.29, L.30, E.31, S.46, P.47, Q.81 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.31, B:Q.81 Hydrogen bonds: B:E.31, B:E.31 V6P.14: 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:P.68 Hydrogen bonds: B:F.66 pi-Cation interactions: B:R.58 V6P.20: 7 residues within 4Å: Chain C: R.29, L.30, E.31, S.46, P.47, Q.81, A.82 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.31 Hydrogen bonds: C:R.29 V6P.26: 7 residues within 4Å: Chain D: R.29, L.30, E.31, S.46, P.47, Q.81, A.82 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.31 Hydrogen bonds: D:R.29

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

CL.17: 4 residues within 4Å: Chain A: T.39, E.40 Chain C: 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: T.39, E.40 Chain D: R.159, R.160 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: R.159, R.160 Chain D: T.39, E.40 Ligand excluded by PLIP

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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