SMTL ID : 4p2y.2 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-4-4-mer

Ligands

24 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.161, E.163 Chain G: D.109 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain G Metal complexes: A:H.161, A:E.163, G:D.109, G:D.109 ZN.2: 4 residues within 4Å: Chain A: D.141, D.182 Ligands: CL.7, CL.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.141, A:D.182 ZN.3: 2 residues within 4Å: Chain A: H.198 Chain C: E.13 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:H.198, C:E.13, H2O.2, H2O.9 ZN.4: 2 residues within 4Å: Chain A: H.251 Ligands: CL.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.251 ZN.16: 4 residues within 4Å: Chain A: E.113 Chain B: H.19, H.29 Ligands: CL.6 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.113, A:E.113, B:H.19, B:H.29 ZN.20: 3 residues within 4Å: Chain B: C.5 Chain F: R.57, D.61 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: B:C.5, F:D.61, H2O.21 ZN.22: 3 residues within 4Å: Chain C: H.161, E.163 Chain E: D.109 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E Metal complexes: C:H.161, C:E.163, E:D.109, E:D.109 ZN.23: 4 residues within 4Å: Chain C: D.141, D.182 Ligands: CL.28, CL.29 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.141, C:D.182 ZN.24: 2 residues within 4Å: Chain A: E.13 Chain C: H.198 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.198, A:E.13, H2O.2, H2O.9 ZN.25: 2 residues within 4Å: Chain C: H.251 Ligands: CL.30 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.251 ZN.37: 4 residues within 4Å: Chain C: E.113 Chain D: H.19, H.29 Ligands: CL.27 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.41: 3 residues within 4Å: Chain D: C.5 Chain H: R.57, D.61 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: H:D.61, D:C.5, H2O.28 ZN.43: 3 residues within 4Å: Chain C: D.109 Chain E: H.161, E.163 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain C Metal complexes: E:H.161, E:E.163, C:D.109, C:D.109 ZN.44: 4 residues within 4Å: Chain E: D.141, D.182 Ligands: CL.49, CL.50 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.141, E:D.182 ZN.45: 2 residues within 4Å: Chain E: H.198 Chain G: E.13 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: E:H.198, G:E.13, H2O.16, H2O.24 ZN.46: 2 residues within 4Å: Chain E: H.251 Ligands: CL.51 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.251 ZN.58: 4 residues within 4Å: Chain E: E.113 Chain F: H.19, H.29 Ligands: CL.48 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Metal complexes: F:H.19, F:H.29, E:E.113, E:E.113 ZN.62: 3 residues within 4Å: Chain B: R.57, D.61 Chain F: C.5 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: F:C.5, B:D.61, H2O.7 ZN.64: 3 residues within 4Å: Chain A: D.109 Chain G: H.161, E.163 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain G Metal complexes: A:D.109, A:D.109, G:H.161, G:E.163 ZN.65: 4 residues within 4Å: Chain G: D.141, D.182 Ligands: CL.70, CL.71 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.141, G:D.182 ZN.66: 2 residues within 4Å: Chain E: E.13 Chain G: H.198 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: G:H.198, E:E.13, H2O.17, H2O.24 ZN.67: 2 residues within 4Å: Chain G: H.251 Ligands: CL.72 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:H.251 ZN.79: 4 residues within 4Å: Chain G: E.113 Chain H: H.19, H.29 Ligands: CL.69 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain G Metal complexes: H:H.19, H:H.29, G:E.113, G:E.113 ZN.83: 3 residues within 4Å: Chain D: R.57, D.61 Chain H: C.5 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: H:C.5, D:D.61, H2O.14

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

CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: E.113, R.209 Chain B: F.18, H.19, H.29 Ligands: ZN.16 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: L.140, D.141, D.182 Ligands: ZN.2, CL.8, ACT.15 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: D.141, D.182 Ligands: ZN.2, CL.7 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: H.251 Ligands: ZN.4 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain F: I.46 Ligand excluded by PLIP CL.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.27: 6 residues within 4Å: Chain C: E.113, R.209 Chain D: F.18, H.19, H.29 Ligands: ZN.37 Ligand excluded by PLIP CL.28: 6 residues within 4Å: Chain C: L.140, D.141, D.182 Ligands: ZN.23, CL.29, ACT.36 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain C: D.141, D.182 Ligands: ZN.23, CL.28 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain C: H.251 Ligands: ZN.25 Ligand excluded by PLIP CL.38: 1 residues within 4Å: Chain H: I.46 Ligand excluded by PLIP CL.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.48: 6 residues within 4Å: Chain E: E.113, R.209 Chain F: F.18, H.19, H.29 Ligands: ZN.58 Ligand excluded by PLIP CL.49: 6 residues within 4Å: Chain E: L.140, D.141, D.182 Ligands: ZN.44, CL.50, ACT.57 Ligand excluded by PLIP CL.50: 4 residues within 4Å: Chain E: D.141, D.182 Ligands: ZN.44, CL.49 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain E: H.251 Ligands: ZN.46 Ligand excluded by PLIP CL.59: 1 residues within 4Å: Chain B: I.46 Ligand excluded by PLIP CL.68: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.69: 6 residues within 4Å: Chain G: E.113, R.209 Chain H: F.18, H.19, H.29 Ligands: ZN.79 Ligand excluded by PLIP CL.70: 6 residues within 4Å: Chain G: L.140, D.141, D.182 Ligands: ZN.65, CL.71, ACT.78 Ligand excluded by PLIP CL.71: 4 residues within 4Å: Chain G: D.141, D.182 Ligands: ZN.65, CL.70 Ligand excluded by PLIP CL.72: 2 residues within 4Å: Chain G: H.251 Ligands: ZN.67 Ligand excluded by PLIP CL.80: 1 residues within 4Å: Chain D: I.46 Ligand excluded by PLIP

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

ACT.10: 6 residues within 4Å: Chain A: T.36, R.38, T.39, W.53, V.56, D.74 Ligand excluded by PLIP ACT.11: 5 residues within 4Å: Chain A: G.51, D.54 Chain H: D.67, Q.68, E.69 Ligand excluded by PLIP ACT.12: 2 residues within 4Å: Chain A: R.58, L.60 Ligand excluded by PLIP ACT.13: 4 residues within 4Å: Chain A: R.209 Chain B: N.71, F.72, Q.73 Ligand excluded by PLIP ACT.14: 6 residues within 4Å: Chain A: G.134, T.135, L.136, E.156, T.158, Q.170 Ligand excluded by PLIP ACT.15: 3 residues within 4Å: Chain A: P.177, P.185 Ligands: CL.7 Ligand excluded by PLIP ACT.21: 2 residues within 4Å: Chain B: K.37, D.52 Ligand excluded by PLIP ACT.31: 6 residues within 4Å: Chain C: T.36, R.38, T.39, W.53, V.56, D.74 Ligand excluded by PLIP ACT.32: 5 residues within 4Å: Chain C: G.51, D.54 Chain F: D.67, Q.68, E.69 Ligand excluded by PLIP ACT.33: 2 residues within 4Å: Chain C: R.58, L.60 Ligand excluded by PLIP ACT.34: 4 residues within 4Å: Chain C: R.209 Chain D: N.71, F.72, Q.73 Ligand excluded by PLIP ACT.35: 6 residues within 4Å: Chain C: G.134, T.135, L.136, E.156, T.158, Q.170 Ligand excluded by PLIP ACT.36: 3 residues within 4Å: Chain C: P.177, P.185 Ligands: CL.28 Ligand excluded by PLIP ACT.42: 2 residues within 4Å: Chain D: K.37, D.52 Ligand excluded by PLIP ACT.52: 6 residues within 4Å: Chain E: T.36, R.38, T.39, W.53, V.56, D.74 Ligand excluded by PLIP ACT.53: 5 residues within 4Å: Chain D: D.67, Q.68, E.69 Chain E: G.51, D.54 Ligand excluded by PLIP ACT.54: 2 residues within 4Å: Chain E: R.58, L.60 Ligand excluded by PLIP ACT.55: 4 residues within 4Å: Chain E: R.209 Chain F: N.71, F.72, Q.73 Ligand excluded by PLIP ACT.56: 6 residues within 4Å: Chain E: G.134, T.135, L.136, E.156, T.158, Q.170 Ligand excluded by PLIP ACT.57: 3 residues within 4Å: Chain E: P.177, P.185 Ligands: CL.49 Ligand excluded by PLIP ACT.63: 2 residues within 4Å: Chain F: K.37, D.52 Ligand excluded by PLIP ACT.73: 6 residues within 4Å: Chain G: T.36, R.38, T.39, W.53, V.56, D.74 Ligand excluded by PLIP ACT.74: 5 residues within 4Å: Chain B: D.67, Q.68, E.69 Chain G: G.51, D.54 Ligand excluded by PLIP ACT.75: 2 residues within 4Å: Chain G: R.58, L.60 Ligand excluded by PLIP ACT.76: 4 residues within 4Å: Chain G: R.209 Chain H: N.71, F.72, Q.73 Ligand excluded by PLIP ACT.77: 6 residues within 4Å: Chain G: G.134, T.135, L.136, E.156, T.158, Q.170 Ligand excluded by PLIP ACT.78: 3 residues within 4Å: Chain G: P.177, P.185 Ligands: CL.70 Ligand excluded by PLIP ACT.84: 2 residues within 4Å: Chain H: K.37, D.52 Ligand excluded by PLIP

8 x CA: CALCIUM ION(Non-covalent)

CA.18: 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.7 CA.19: 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.39: 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.14 CA.40: 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.14 CA.60: 5 residues within 4Å: Chain F: D.63, N.65, D.67, E.69, E.74 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.63, F:D.67, F:E.69, F:E.74, H2O.22 CA.61: 5 residues within 4Å: Chain F: S.22, E.25, D.27, T.30, E.35 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:S.22, F:E.25, F:D.27, F:T.30, H2O.21 CA.81: 5 residues within 4Å: Chain H: D.63, N.65, D.67, E.69, E.74 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.63, H:D.67, H:E.69, H:E.74, H2O.29 CA.82: 5 residues within 4Å: Chain H: S.22, E.25, D.27, T.30, E.35 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:S.22, H:E.25, H:D.27, H:T.30, H2O.28

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

2015-03-11

Peptides

Advanced glycosylation end product-specific receptor: ACEG
Protein S100-A6: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
B

D
B

F
B

H
B

Advanced glycosylation end product-specific receptor

Protein S100-A6

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