SMTL ID : 6xq9.1 (1 other biounit)

Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

2 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 Ligands: ACT.2 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: 4 residues within 4Å: Chain A: A.2, R.79 Ligands: ACT.1, V6M.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.2 Salt bridges: A:R.79

2 x V6S: 4-(3-hydroxyphenoxy)benzoic acid(Non-covalent)

V6S.3: 7 residues within 4Å: Chain A: R.29, L.30, E.31, Q.81, A.82, M.83, E.89 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.29, A:R.29, A:E.31 Hydrogen bonds: A:E.89 V6S.4: 7 residues within 4Å: Chain A: D.54, S.55, R.58, V.59, L.60, P.61, F.66 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.58, A:L.60, A:F.66 pi-Cation interactions: A:R.58

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

V6M.5: 10 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.2, A:E.31, A:K.33, A:R.79, A:Q.81, A:K.91, A:K.91, A:N.93 Salt bridges: A:K.33 pi-Cation interactions: A:K.33, A:R.79, A: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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Advanced glycosylation end product-specific receptor

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