SMTL ID : 2h61.1

X-ray structure of human Ca2+-loaded S100B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-octamer

Ligands

18 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.19, A:E.22, A:D.24, A:K.27, H2O.1 CA.2: 5 residues within 4Å: Chain A: D.62, D.64, D.66, E.68, E.73 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.64, A:D.66, A:E.68, A:E.73, A:E.73 CA.3: 5 residues within 4Å: Chain B: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.19, B:E.22, B:D.24, B:K.27, H2O.4 CA.4: 5 residues within 4Å: Chain B: D.62, D.64, D.66, E.68, E.73 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.62, B:E.68, B:E.73, B:E.73, H2O.5 CA.5: 5 residues within 4Å: Chain C: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.19, C:E.22, C:D.24, C:K.27, H2O.7 CA.6: 5 residues within 4Å: Chain C: D.62, D.64, D.66, E.68, E.73 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.62, C:D.66, C:E.73, C:E.73, H2O.7 CA.7: 5 residues within 4Å: Chain D: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.19, D:E.22, D:D.24, D:K.27, H2O.10 CA.8: 5 residues within 4Å: Chain D: D.62, D.64, D.66, E.68, E.73 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.62, D:E.68, D:E.73, D:E.73, H2O.10 CA.9: 3 residues within 4Å: Chain D: D.13 Chain E: S.42, L.45 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: D:D.13, E:S.42, E:L.45, H2O.10, H2O.13 CA.10: 5 residues within 4Å: Chain E: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:S.19, E:D.24, E:K.27, E:E.32, H2O.13 CA.11: 5 residues within 4Å: Chain E: D.62, D.64, D.66, E.68, E.73 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.62, E:D.66, E:E.68, E:E.73, H2O.13 CA.13: 5 residues within 4Å: Chain F: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:S.19, F:D.24, F:K.27, F:E.32, H2O.16 CA.14: 5 residues within 4Å: Chain F: D.62, D.64, D.66, E.68, E.73 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.62, F:D.64, F:D.66, F:E.68, H2O.18 CA.15: 5 residues within 4Å: Chain G: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:S.19, G:E.22, G:D.24, G:K.27, H2O.19 CA.16: 5 residues within 4Å: Chain G: D.62, D.64, D.66, E.68, E.73 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.62, G:E.68, G:E.73, G:E.73, H2O.18 CA.17: 2 residues within 4Å: Chain B: S.42 Chain G: D.13 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: B:S.42, G:D.13, H2O.4, H2O.18 CA.18: 5 residues within 4Å: Chain H: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:S.19, H:E.22, H:D.24, H:K.27, H2O.21 CA.19: 5 residues within 4Å: Chain H: D.62, D.64, D.66, E.68, E.73 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.62, H:E.68, H:E.73, H:E.73, H2O.21

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.12: 10 residues within 4Å: Chain C: F.89 Chain D: V.9, I.12, D.13, H.16 Chain E: H.43, F.44, A.84, C.85, F.88 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ostendorp, T. et al., Structural and functional insights into RAGE activation by multimeric S100B. Embo J. (2007)

Release Date

2007-06-05

Peptides

Protein S100-B: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Protein S100-B

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