SMTL ID : 3m0w.1 (5 other biounits)

Structure of S100A4 with PCP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-10-mer

Ligands

12 x P77: 2-chloro-10-[3-(4-methylpiperazin-1-yl)propyl]-10H-phenothiazine(Non-covalent)

P77.1: 11 residues within 4Å: Chain A: D.9, S.13 Chain B: F.88 Chain I: E.5, L.8, D.9 Chain J: S.43, F.44, C.85, F.88 Ligands: P77.27 6 PLIP interactions: 1 interactions with chain J, 3 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: J:F.88, I:E.5, I:L.8 Hydrogen bonds: A:S.13 Salt bridges: A:D.9, A:D.9 P77.5: 11 residues within 4Å: Chain A: F.88 Chain B: D.9, S.13 Chain C: S.43, F.44, C.85, F.88, F.89 Chain D: E.5, D.9 Ligands: P77.12 8 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B, 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:F.88, A:F.88, C:F.88, C:F.89, D:E.5 Hydrogen bonds: B:S.13 Salt bridges: B:D.9, B:D.9 P77.8: 8 residues within 4Å: Chain B: F.44, M.84, C.85, E.87, F.92 Chain J: F.88, F.92 Ligands: P77.27 8 PLIP interactions: 5 interactions with chain J, 3 interactions with chain B Hydrophobic interactions: J:F.88, J:F.92, J:F.92, B:M.84, B:F.92 pi-Stacking: J:F.88, J:F.88 Salt bridges: B:E.87 P77.9: 11 residues within 4Å: Chain C: D.9, S.13 Chain D: F.88 Chain E: S.43, F.44, I.81, C.85 Chain F: E.5, L.8, D.9 Ligands: P77.18 9 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C, 2 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: D:F.88, D:F.88, E:I.81, F:L.8 Hydrogen bonds: C:S.13, E:S.43 Salt bridges: C:D.9, C:D.9, F:E.5 P77.12: 12 residues within 4Å: Chain A: S.43, F.44, C.85, F.88, F.89 Chain B: E.5, L.8, D.9 Chain C: F.88 Chain D: D.9, S.13 Ligands: P77.5 9 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: A:F.88, A:F.89, B:E.5, B:L.8, C:F.88, C:F.88 Hydrogen bonds: D:S.13 Salt bridges: D:D.9, D:D.9 P77.15: 11 residues within 4Å: Chain E: D.9, S.13 Chain F: F.88 Chain G: S.43, F.44, C.85, F.88 Chain H: E.5, L.8, D.9 Ligands: P77.24 7 PLIP interactions: 3 interactions with chain E, 1 interactions with chain G, 2 interactions with chain H, 1 interactions with chain F Hydrogen bonds: E:S.13 Salt bridges: E:D.9, E:D.9 Hydrophobic interactions: G:F.88, H:L.8, H:L.8, F:F.88 P77.18: 11 residues within 4Å: Chain C: E.5, L.8, D.9 Chain D: S.43, I.81, C.85, F.88 Chain E: F.88 Chain F: D.9, S.13 Ligands: P77.9 8 PLIP interactions: 3 interactions with chain F, 2 interactions with chain D, 2 interactions with chain E, 1 interactions with chain C Hydrogen bonds: F:S.13 Salt bridges: F:D.9, F:D.9 Hydrophobic interactions: D:F.88, E:F.88, E:F.88, C:L.8 pi-Stacking: D:F.88 P77.21: 12 residues within 4Å: Chain G: D.9 Chain H: F.88 Chain I: S.43, F.44, I.81, C.85, F.88 Chain J: E.5, L.8, D.9 Ligands: P77.28, P77.31 7 PLIP interactions: 2 interactions with chain I, 2 interactions with chain H, 1 interactions with chain J, 2 interactions with chain G Hydrophobic interactions: I:I.81, I:F.88, H:F.88, H:F.88, J:L.8 Salt bridges: G:D.9, G:D.9 P77.24: 13 residues within 4Å: Chain E: E.5, L.8, D.9 Chain F: S.43, F.44, I.81, C.85, F.88, F.89 Chain G: F.88 Chain H: D.9, S.13 Ligands: P77.15 7 PLIP interactions: 3 interactions with chain F, 3 interactions with chain H, 1 interactions with chain E Hydrophobic interactions: F:I.81, F:F.88, F:F.89, E:L.8 Hydrogen bonds: H:S.13 Salt bridges: H:D.9, H:D.9 P77.27: 13 residues within 4Å: Chain A: E.5, L.8, D.9 Chain B: S.43, F.44, I.81, C.85, F.88 Chain I: D.9, S.13 Chain J: F.88 Ligands: P77.1, P77.8 7 PLIP interactions: 3 interactions with chain I, 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain J Hydrogen bonds: I:S.13 Salt bridges: I:D.9, I:D.9 Hydrophobic interactions: A:L.8, A:L.8, B:F.88, J:F.88 P77.28: 8 residues within 4Å: Chain H: F.88, F.89 Chain I: S.43, F.44, G.46, M.84, C.85 Ligands: P77.21 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: I:F.44, I:M.84 pi-Stacking: H:F.88 P77.31: 11 residues within 4Å: Chain G: E.5, L.8, D.9 Chain H: S.43, F.44, C.85, F.88 Chain I: F.88 Chain J: D.9, S.13 Ligands: P77.21 8 PLIP interactions: 1 interactions with chain H, 3 interactions with chain J, 2 interactions with chain I, 2 interactions with chain G Hydrophobic interactions: H:F.88, I:F.88, I:F.88, G:L.8, G:L.8 Hydrogen bonds: J:S.13 Salt bridges: J:D.9, J:D.9

20 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.19, A:E.22, A:D.24, A:K.27, A:E.32 CA.3: 5 residues within 4Å: Chain A: D.62, N.64, D.66, E.68, E.73 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.62, A:D.66, A:E.68, A:E.73, A:E.73 CA.6: 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.1 CA.7: 5 residues within 4Å: Chain B: D.62, N.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:D.66, B:E.68, B:E.73, H2O.1 CA.10: 7 residues within 4Å: Chain C: S.19, G.20, K.21, E.22, D.24, K.27, E.32 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:S.19, C:E.22, C:D.24, C:E.32, C:E.32 CA.11: 5 residues within 4Å: Chain C: D.62, N.64, D.66, E.68, E.73 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.62, C:D.66, C:E.68, C:E.73, C:E.73 CA.13: 6 residues within 4Å: Chain D: S.19, E.22, G.23, D.24, K.27, E.32 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:S.19, D:E.22, D:D.24, D:K.27, D:E.32 CA.14: 5 residues within 4Å: Chain D: D.62, N.64, D.66, E.68, E.73 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.62, D:D.66, D:E.68, D:E.73, D:E.73 CA.16: 6 residues within 4Å: Chain E: S.19, E.22, K.27, L.28, N.29, E.32 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:K.27 CA.17: 6 residues within 4Å: Chain E: L.61, D.62, S.63, N.64, D.66, E.68 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.62 CA.19: 7 residues within 4Å: Chain F: S.19, E.22, D.24, K.27, L.28, N.29, E.32 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:S.19, F:D.24, F:K.27, F:E.32, F:E.32 CA.20: 5 residues within 4Å: Chain F: D.62, N.64, D.66, E.68, E.73 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.62, F:D.66, F:E.68, F:E.73, F:E.73 CA.22: 5 residues within 4Å: Chain G: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:S.19, G:E.22, G:D.24, G:K.27, G:E.32 CA.23: 5 residues within 4Å: Chain G: D.62, N.64, D.66, E.68, E.73 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.62, G:D.66, G:E.73 CA.25: 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.1 CA.26: 6 residues within 4Å: Chain H: D.62, N.64, D.66, E.68, D.70, E.73 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.62, H:D.66, H:E.68, H:E.73 CA.29: 5 residues within 4Å: Chain I: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:S.19, I:E.22, I:D.24, I:K.27, I:E.32 CA.30: 5 residues within 4Å: Chain I: D.62, N.64, D.66, E.68, E.73 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.62, I:D.66, I:E.68, I:E.73, H2O.1 CA.32: 5 residues within 4Å: Chain J: S.19, E.22, D.24, K.27, E.32 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:S.19, J:E.22, J:K.27, J:E.32, H2O.1 CA.33: 5 residues within 4Å: Chain J: D.62, N.64, D.66, E.68, E.73 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.62, J:D.66, J:E.68, J:E.73, H2O.1

2 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.4: 2 residues within 4Å: Chain A: M.84 Chain C: F.88 No protein-ligand interaction detected (PLIP) DIO.34: 2 residues within 4Å: Chain B: F.88 Chain J: M.84 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramagopal, U.A. et al., Structure of S100A4 with PCP. To be published

Release Date

2010-05-12

Peptides

Protein S100-A4: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Protein S100-A4

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