SMTL ID : 4ybh.1

Crystal structure of the human RAGE ectodomain (VC1C2 fragment) in complex with human S100A6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-mer

Ligands

14 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.141, D.182 Ligands: CL.6, CL.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.141, A:D.182 ZN.2: 2 residues within 4Å: Chain A: H.161, E.163 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.161, A:E.163, A:E.163 ZN.3: 1 residues within 4Å: Chain A: H.198 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.198, H2O.2 ZN.4: 3 residues within 4Å: Chain A: H.251, L.261 Ligands: CL.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.251, H2O.2 ZN.12: 4 residues within 4Å: Chain A: E.113 Chain B: H.19, H.29 Ligands: CL.5 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.19, B:H.29, A:E.113, A:E.113 ZN.13: 4 residues within 4Å: Chain B: C.5, P.6 Chain D: R.57, D.61 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:D.61, B:C.5, H2O.15, H2O.15 ZN.14: 2 residues within 4Å: Chain B: E.43 Ligands: CL.15 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.43, B:E.43 ZN.18: 4 residues within 4Å: Chain C: D.141, D.182 Ligands: CL.23, CL.24 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.141, C:D.182 ZN.19: 2 residues within 4Å: Chain C: H.161, E.163 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.161, C:E.163, C:E.163 ZN.20: 1 residues within 4Å: Chain C: H.198 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.198, H2O.10 ZN.21: 3 residues within 4Å: Chain C: H.251, L.261 Ligands: CL.25 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.251, H2O.10 ZN.29: 4 residues within 4Å: Chain C: E.113 Chain D: H.19, H.29 Ligands: CL.22 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Metal complexes: D:H.19, D:H.29, C:E.113, C:E.113 ZN.30: 4 residues within 4Å: Chain B: R.57, D.61 Chain D: C.5, P.6 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:C.5, B:D.61, H2O.7, H2O.7 ZN.31: 2 residues within 4Å: Chain D: E.43 Ligands: CL.32 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.43, D:E.43

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

CL.5: 6 residues within 4Å: Chain A: E.113, R.209 Chain B: F.18, H.19, H.29 Ligands: ZN.12 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: L.140, D.141, D.182, P.185 Ligands: ZN.1, CL.7 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: D.141, D.182 Ligands: ZN.1, CL.6 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: H.251 Ligands: ZN.4 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: E.43 Ligands: ZN.14 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain C: E.113, R.209 Chain D: F.18, H.19, H.29 Ligands: ZN.29 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain C: L.140, D.141, D.182, P.185 Ligands: ZN.18, CL.24 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain C: D.141, D.182 Ligands: ZN.18, CL.23 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain C: H.251 Ligands: ZN.21 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain D: E.43 Ligands: ZN.31 Ligand excluded by PLIP

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

ACT.9: 3 residues within 4Å: Chain A: K.150, P.177, P.185 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.177, A:P.185 Salt bridges: A:K.150 ACT.10: 2 residues within 4Å: Chain A: R.58, L.60 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.60 Salt bridges: A:R.58 ACT.11: 7 residues within 4Å: Chain A: L.34, T.36, R.38, T.39, W.53, V.56, D.74 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.34, A:T.39, A:W.53 Hydrogen bonds: A:D.74 ACT.26: 3 residues within 4Å: Chain C: K.150, P.177, P.185 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.177, C:P.185 Salt bridges: C:K.150 ACT.27: 2 residues within 4Å: Chain C: R.58, L.60 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.60 Salt bridges: C:R.58 ACT.28: 7 residues within 4Å: Chain C: L.34, T.36, R.38, T.39, W.53, V.56, D.74 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.34, C:T.39, C:W.53 Hydrogen bonds: C:T.36

4 x CA: CALCIUM ION(Non-covalent)

CA.16: 5 residues within 4Å: Chain B: S.22, E.25, D.27, T.30, E.35 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.22, B:E.25, B:D.27, B:T.30, H2O.7 CA.17: 5 residues within 4Å: Chain B: D.63, N.65, D.67, E.69, E.74 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.63, B:D.67, B:E.69, B:E.74, H2O.8 CA.33: 5 residues within 4Å: Chain D: S.22, E.25, D.27, T.30, E.35 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.22, D:E.25, D:D.27, D:T.30, H2O.15 CA.34: 5 residues within 4Å: Chain D: D.63, N.65, D.67, E.69, E.74 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.63, D:D.67, D:E.69, D:E.74, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yatime, L. et al., The Structure of the RAGE:S100A6 Complex Reveals a Unique Mode of Homodimerization for S100 Proteins. Structure (2016)

Release Date

2016-03-02

Peptides

Advanced glycosylation end product-specific receptor: AC
Protein S100-A6: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Advanced glycosylation end product-specific receptor

Protein S100-A6

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