SMTL ID : 1v6p.1

Crystal structure of Cobrotoxin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.87 Å

Oligo State

homo-dimer

Ligands

12 x CU: COPPER (II) ION(Non-covalent)(Non-functional Binders)

CU.1: 2 residues within 4Å: Chain A: H.4, N.62 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.4, H2O.1 CU.2: 3 residues within 4Å: Chain A: E.2, D.58 Ligands: CU.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.2, A:D.58, A:D.58, H2O.1, H2O.1 CU.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CU.4: 1 residues within 4Å: Chain A: R.59 No protein-ligand interaction detected (PLIP) CU.5: 2 residues within 4Å: Chain A: D.31 Chain B: D.58 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.58, B:D.58, A:D.31, H2O.8, H2O.8 CU.6: 2 residues within 4Å: Chain A: E.2 Ligands: CU.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.2, H2O.1, H2O.1, H2O.1, H2O.4 CU.7: 5 residues within 4Å: Chain A: K.47 Chain B: H.4, P.12, T.13, T.14 No protein-ligand interaction detected (PLIP) CU.8: 3 residues within 4Å: Chain A: S.8, R.36, T.37 No protein-ligand interaction detected (PLIP) CU.9: 2 residues within 4Å: Chain A: N.48 Ligands: EOH.14 No protein-ligand interaction detected (PLIP) CU.10: 2 residues within 4Å: Chain A: L.1, G.19 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.19, H2O.1, H2O.2 CU.16: 5 residues within 4Å: Chain A: E.38 Chain B: H.4, R.59, N.62 Ligands: CL.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.4, B:R.59, A:E.38, A:E.38 CU.17: 1 residues within 4Å: Chain B: W.29 No protein-ligand interaction detected (PLIP)

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

CL.11: 6 residues within 4Å: Chain A: K.27, W.29, E.38 Chain B: H.4, R.59 Ligands: CU.16 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.12: 1 residues within 4Å: Chain A: N.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.62, A:N.62 NA.13: 2 residues within 4Å: Chain A: T.14, R.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.14, A:T.14

2 x EOH: ETHANOL(Non-functional Binders)

EOH.14: 3 residues within 4Å: Chain A: K.47, N.48 Ligands: CU.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.47 Hydrogen bonds: A:N.48 Water bridges: A:N.48 EOH.15: 4 residues within 4Å: Chain A: C.43, S.45, V.46, I.52 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.52 Hydrogen bonds: A:V.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lou, X. et al., The atomic resolution crystal structure of atratoxin determined by single wavelength anomalous diffraction phasing. J.Biol.Chem. (2004)

Release Date

2004-12-21

Peptides

Cobrotoxin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cobrotoxin

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