SMTL ID : 3n7x.3 (5 other biounits)

Crystal structure of Penaeus stylirostris densovirus capsid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-pentamer

Ligands

5 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: E.191 Chain B: Y.55, Q.176 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.191, B:Y.55, B:Q.176, H2O.7, H2O.10 CA.4: 3 residues within 4Å: Chain B: E.191 Chain C: Y.55, Q.176 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:Y.55, C:Q.176, B:E.191, H2O.13, H2O.16 CA.7: 3 residues within 4Å: Chain C: E.191 Chain D: Y.55, Q.176 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:Y.55, D:Q.176, C:E.191, H2O.19, H2O.22 CA.10: 3 residues within 4Å: Chain D: E.191 Chain E: Y.55, Q.176 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: E:Y.55, E:Q.176, D:E.191, H2O.25, H2O.28 CA.13: 3 residues within 4Å: Chain A: Y.55, Q.176 Chain E: E.191 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: A:Y.55, A:Q.176, E:E.191, H2O.1, H2O.4

10 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: H.77, W.78, F.232, C.323, Y.324 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: E.139 Chain E: N.275 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain B: H.77, W.78, F.232, C.323, Y.324 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: N.275 Chain B: E.139 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain C: H.77, W.78, F.232, C.323, Y.324 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: N.275 Chain C: E.139 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain D: H.77, W.78, F.232, C.323, Y.324 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain C: N.275 Chain D: E.139 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain E: H.77, W.78, F.232, C.323, Y.324 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain D: N.275 Chain E: E.139 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaufmann, B. et al., Structure of Penaeus stylirostris densovirus, a shrimp pathogen. J.Virol. (2010)

Release Date

2010-11-17

Peptides

Capsid protein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

Capsid protein

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