SMTL ID : 2nxq.3 (4 other biounits)

Crystal structure of calcium binding protein 1 from Entamoeba histolytica: a novel arrangement of EF hand motifs

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

12 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.10, N.12, D.14, A.16, E.21 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.10, A:D.14, A:A.16, A:E.21, H2O.1 CA.2: 5 residues within 4Å: Chain A: D.46, D.48, N.50, E.52, E.57 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.46, A:D.48, A:E.52, A:E.57, A:E.57 CA.5: 5 residues within 4Å: Chain B: D.10, N.12, D.14, A.16, E.21 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.10, B:D.14, B:A.16, B:E.21, H2O.2 CA.6: 5 residues within 4Å: Chain B: D.46, D.48, N.50, E.52, E.57 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.46, B:D.48, B:E.52, B:E.57, H2O.2 CA.10: 5 residues within 4Å: Chain C: D.10, N.12, D.14, A.16, E.21 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.10, C:D.14, C:A.16, C:E.21, H2O.2 CA.11: 5 residues within 4Å: Chain C: D.46, D.48, N.50, E.52, E.57 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.46, C:D.48, C:E.52, C:E.57, C:E.57 CA.14: 5 residues within 4Å: Chain D: D.10, N.12, D.14, A.16, E.21 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.10, D:D.14, D:A.16, D:E.21, H2O.3 CA.15: 5 residues within 4Å: Chain D: D.46, D.48, N.50, E.52, E.57 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.46, D:D.48, D:E.52, D:E.57, H2O.3 CA.19: 5 residues within 4Å: Chain E: D.10, N.12, D.14, A.16, E.21 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.10, E:D.14, E:A.16, E:E.21, H2O.3 CA.20: 5 residues within 4Å: Chain E: D.46, D.48, N.50, E.52, E.57 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.46, E:D.48, E:E.52, E:E.57, E:E.57 CA.23: 5 residues within 4Å: Chain F: D.10, N.12, D.14, A.16, E.21 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.10, F:D.14, F:A.16, F:E.21, H2O.4 CA.24: 5 residues within 4Å: Chain F: D.46, D.48, N.50, E.52, E.57 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.46, F:D.48, F:E.52, F:E.57, H2O.4

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

ACT.3: 1 residues within 4Å: Chain A: Y.62 No protein-ligand interaction detected (PLIP) ACT.4: 2 residues within 4Å: Chain A: K.33, L.40 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.40 Salt bridges: A:K.33 ACT.7: 1 residues within 4Å: Chain B: Y.62 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.62 ACT.8: 2 residues within 4Å: Chain B: L.40 Chain C: F.61 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.40, C:F.61 Salt bridges: B:K.33 ACT.9: 2 residues within 4Å: Chain B: V.26 Chain F: L.37 No protein-ligand interaction detected (PLIP) ACT.12: 1 residues within 4Å: Chain C: Y.62 No protein-ligand interaction detected (PLIP) ACT.13: 2 residues within 4Å: Chain C: K.33, L.40 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.40 Salt bridges: C:K.33 ACT.16: 1 residues within 4Å: Chain D: Y.62 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.62 ACT.17: 2 residues within 4Å: Chain D: L.40 Chain E: F.61 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:F.61, D:L.40 Salt bridges: D:K.33 ACT.18: 2 residues within 4Å: Chain B: L.37 Chain D: V.26 No protein-ligand interaction detected (PLIP) ACT.21: 1 residues within 4Å: Chain E: Y.62 No protein-ligand interaction detected (PLIP) ACT.22: 2 residues within 4Å: Chain E: K.33, L.40 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.40 Salt bridges: E:K.33 ACT.25: 1 residues within 4Å: Chain F: Y.62 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.62 ACT.26: 2 residues within 4Å: Chain A: F.61 Chain F: L.40 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:F.61, F:L.40 Salt bridges: F:K.33 ACT.27: 2 residues within 4Å: Chain D: L.37 Chain F: V.26 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, S. et al., Crystal structure of calcium binding protein-1 from Entamoeba histolytica: A novel arrangement of EF hand motifs. Proteins (2007)

Release Date

2007-08-21

Peptides

Calcium-binding protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Calcium-binding protein

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