SMTL ID : 1lnl.1

Structure of deoxygenated hemocyanin from Rapana thomasiana

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-hexamer

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG.1: 5 residues within 4Å: Chain A: R.11, N.12, L.13, S.14, P.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.12 NAG.8: 4 residues within 4Å: Chain C: D.115, N.122, F.123 Ligands: NAG.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.115, C:N.122, C:N.122 NAG.9: 1 residues within 4Å: Ligands: NAG.8 No protein-ligand interaction detected (PLIP) NAG.13: 5 residues within 4Å: Chain D: R.11, N.12, L.13, S.14, P.15 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.12 NAG.20: 4 residues within 4Å: Chain F: D.115, N.122, F.123 Ligands: NAG.21 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.115, F:N.122, F:N.122 NAG.21: 1 residues within 4Å: Ligands: NAG.20 No protein-ligand interaction detected (PLIP)

18 x CU: COPPER (II) ION(Non-covalent)

CU.2: 5 residues within 4Å: Chain A: H.44, C.62, H.64, H.73 Ligands: CU.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.44, A:H.64, A:H.73 CU.3: 5 residues within 4Å: Chain A: H.73, H.184, H.188, H.215 Ligands: CU.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.73, A:H.184, A:H.188, A:H.215 CU.4: 1 residues within 4Å: Chain B: H.120 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.120 CU.5: 6 residues within 4Å: Chain B: H.44, H.64, H.73, H.184, H.215 Ligands: CU.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.44, B:H.64, B:H.73 CU.6: 6 residues within 4Å: Chain B: H.73, H.184, H.188, F.211, H.215 Ligands: CU.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.184, B:H.188, B:H.215 CU.7: 2 residues within 4Å: Chain B: H.2, R.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.2 CU.10: 5 residues within 4Å: Chain C: H.44, H.64, H.73, H.184 Ligands: CU.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.44, C:H.64, C:H.73 CU.11: 5 residues within 4Å: Chain C: H.73, H.184, H.188, H.215 Ligands: CU.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.184, C:H.184, C:H.188, C:H.215 CU.12: 2 residues within 4Å: Chain C: H.2, R.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.2, C:H.2 CU.14: 5 residues within 4Å: Chain D: H.44, C.62, H.64, H.73 Ligands: CU.15 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.44, D:H.64, D:H.73 CU.15: 5 residues within 4Å: Chain D: H.73, H.184, H.188, H.215 Ligands: CU.14 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.73, D:H.184, D:H.188, D:H.215 CU.16: 1 residues within 4Å: Chain E: H.120 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.120 CU.17: 6 residues within 4Å: Chain E: H.44, H.64, H.73, H.184, H.215 Ligands: CU.18 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.44, E:H.64, E:H.73 CU.18: 6 residues within 4Å: Chain E: H.73, H.184, H.188, F.211, H.215 Ligands: CU.17 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.184, E:H.188, E:H.215 CU.19: 2 residues within 4Å: Chain E: H.2, R.3 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.2 CU.22: 5 residues within 4Å: Chain F: H.44, H.64, H.73, H.184 Ligands: CU.23 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.44, F:H.64, F:H.73 CU.23: 5 residues within 4Å: Chain F: H.73, H.184, H.188, H.215 Ligands: CU.22 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.184, F:H.184, F:H.188, F:H.215 CU.24: 2 residues within 4Å: Chain F: H.2, R.3 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.2, F:H.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perbandt, M. et al., The structure of a functional unit from the wall of a gastropod hemocyanin offers a possible mechanism for cooperativity. Biochemistry (2003)

Release Date

2003-06-03

Peptides

hemocyanin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

hemocyanin