SMTL ID : 1z1c.3 (3 other biounits)

Structural Determinants of Tissue Tropism and In Vivo Pathogenicity for the Parvovirus Minute virus of Mice

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-hexamer

Ligands

6 x DA- DC- DA- DC- DC- DA- DA- DA- DA: 5'-D(*AP*CP*AP*CP*CP*AP*AP*AP*A)-3'(Non-covalent)

DA-DC-DA-DC-DC-DA-DA-DA-DA.1: 10 residues within 4Å: Chain A: C.3, C.4, T.9, A.11, C.12 Chain F: W.60, Q.137, N.139, P.276, R.534 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:A.539, F:T.541 Hydrogen bonds: F:D.58, B:Y.53, B:Y.53, B:Y.53 Water bridges: F:D.58, F:D.58 DA-DC-DA-DC-DC-DA-DA-DA-DA.5: 12 residues within 4Å: Chain B: Y.271, D.273 Chain C: C.3, C.4, T.9, A.11, C.12 Chain J: W.60, Q.137, N.139, P.276, R.534 Protein-ligand interaction information (PLIP) not available DA-DC-DA-DC-DC-DA-DA-DA-DA.9: 12 residues within 4Å: Chain B: W.60, Q.137, N.139, P.276, R.534 Chain E: C.3, C.4, T.9, A.11, C.12 Chain H: Y.271, D.273 Protein-ligand interaction information (PLIP) not available DA-DC-DA-DC-DC-DA-DA-DA-DA.13: 10 residues within 4Å: Chain G: C.3, C.4, T.9, A.11, C.12 Chain L: W.60, Q.137, N.139, P.276, R.534 Protein-ligand interaction information (PLIP) not available DA-DC-DA-DC-DC-DA-DA-DA-DA.17: 10 residues within 4Å: Chain D: W.60, Q.137, N.139, P.276, R.534 Chain I: C.3, C.4, T.9, A.11, C.12 Protein-ligand interaction information (PLIP) not available DA-DC-DA-DC-DC-DA-DA-DA-DA.21: 12 residues within 4Å: Chain H: W.60, Q.137, N.139, P.276, R.534 Chain J: Y.271, D.273 Chain K: C.3, C.4, T.9, A.11, C.12 Protein-ligand interaction information (PLIP) not available

12 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: C.4, C.6, T.7, T.9 No protein-ligand interaction detected (PLIP) CA.3: 3 residues within 4Å: Chain A: T.2, C.3, T.9 No protein-ligand interaction detected (PLIP) CA.6: 5 residues within 4Å: Chain B: N.183 Chain C: C.4, C.6, T.7, T.9 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain C: T.2, C.3, T.9 No protein-ligand interaction detected (PLIP) CA.10: 5 residues within 4Å: Chain E: C.4, C.6, T.7, T.9 Chain H: N.183 No protein-ligand interaction detected (PLIP) CA.11: 3 residues within 4Å: Chain E: T.2, C.3, T.9 No protein-ligand interaction detected (PLIP) CA.14: 4 residues within 4Å: Chain G: C.4, C.6, T.7, T.9 No protein-ligand interaction detected (PLIP) CA.15: 3 residues within 4Å: Chain G: T.2, C.3, T.9 No protein-ligand interaction detected (PLIP) CA.18: 4 residues within 4Å: Chain I: C.4, C.6, T.7, T.9 No protein-ligand interaction detected (PLIP) CA.19: 3 residues within 4Å: Chain I: T.2, C.3, T.9 No protein-ligand interaction detected (PLIP) CA.22: 5 residues within 4Å: Chain J: N.183 Chain K: C.4, C.6, T.7, T.9 No protein-ligand interaction detected (PLIP) CA.23: 3 residues within 4Å: Chain K: T.2, C.3, T.9 No protein-ligand interaction detected (PLIP)

6 x D5M: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-functional Binders)

D5M.4: 4 residues within 4Å: Chain A: A.8, C.10, A.11, C.12 No protein-ligand interaction detected (PLIP) D5M.8: 4 residues within 4Å: Chain C: A.8, C.10, A.11, C.12 No protein-ligand interaction detected (PLIP) D5M.12: 4 residues within 4Å: Chain E: A.8, C.10, A.11, C.12 No protein-ligand interaction detected (PLIP) D5M.16: 4 residues within 4Å: Chain G: A.8, C.10, A.11, C.12 No protein-ligand interaction detected (PLIP) D5M.20: 4 residues within 4Å: Chain I: A.8, C.10, A.11, C.12 No protein-ligand interaction detected (PLIP) D5M.24: 4 residues within 4Å: Chain K: A.8, C.10, A.11, C.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kontou, M. et al., Structural determinants of tissue tropism and in vivo pathogenicity for the parvovirus minute virus of mice. J.Virol. (2005)

Release Date

2005-09-06

Peptides

Coat protein VP2: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

D
A

F
A

H
A

J
A

L
A

Coat protein VP2

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