SMTL ID : 1rb8.2 (4 other biounits)

The phiX174 DNA binding protein J in two different capsid environments.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-5-5-5-mer

Ligands

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

DC-DA-DA-DA.1: 13 residues within 4Å: Chain A: H.204, E.208, F.212 Chain C: A.27, R.28, Y.31, G.34, Q.35 Chain D: T.423, R.425, D.426 Ligands: DC.2, DC.5 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DA.8: 13 residues within 4Å: Chain D: H.204, E.208, F.212 Chain F: A.27, R.28, Y.31, G.34, Q.35 Chain G: T.423, R.425, D.426 Ligands: DC.9, DC.12 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DA.15: 13 residues within 4Å: Chain G: H.204, E.208, F.212 Chain I: A.27, R.28, Y.31, G.34, Q.35 Chain J: T.423, R.425, D.426 Ligands: DC.16, DC.19 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DA.22: 13 residues within 4Å: Chain J: H.204, E.208, F.212 Chain L: A.27, R.28, Y.31, G.34, Q.35 Chain M: T.423, R.425, D.426 Ligands: DC.23, DC.26 Protein-ligand interaction information (PLIP) not available DC-DA-DA-DA.29: 13 residues within 4Å: Chain A: T.423, R.425, D.426 Chain M: H.204, E.208, F.212 Chain O: A.27, R.28, Y.31, G.34, Q.35 Ligands: DC.30, DC.33 Protein-ligand interaction information (PLIP) not available

30 x DC: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-functional Binders)(Non-covalent)(Covalent)

DC.2: 1 residues within 4Å: Ligands: DC-DA-DA-DA.1 16 PLIP interactions: 3 interactions with chain G, 4 interactions with chain A, 2 interactions with chain F, 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: G:F.277, A:F.277, D:F.277 Salt bridges: G:R.10, G:R.412, A:R.10, F:K.21, D:R.10, D:R.412, C:K.21 Hydrogen bonds: A:K.167, A:D.242, F:Q.36, D:K.167, D:D.242, C:Q.36 DC.3: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available DC.4: 2 residues within 4Å: Chain A: R.10, F.277 Protein-ligand interaction information (PLIP) not available DC.5: 4 residues within 4Å: Chain A: K.167 Chain C: Q.35, Q.36 Ligands: DC-DA-DA-DA.1 Protein-ligand interaction information (PLIP) not available DC.6: 2 residues within 4Å: Chain A: D.242 Chain C: K.25 Protein-ligand interaction information (PLIP) not available DC.7: 5 residues within 4Å: Chain C: R.18, K.21 Chain D: V.47, R.412, N.414 Protein-ligand interaction information (PLIP) not available DC.9: 1 residues within 4Å: Ligands: DC-DA-DA-DA.8 Protein-ligand interaction information (PLIP) not available DC.10: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available DC.11: 2 residues within 4Å: Chain D: R.10, F.277 Protein-ligand interaction information (PLIP) not available DC.12: 4 residues within 4Å: Chain D: K.167 Chain F: Q.35, Q.36 Ligands: DC-DA-DA-DA.8 Protein-ligand interaction information (PLIP) not available DC.13: 2 residues within 4Å: Chain D: D.242 Chain F: K.25 Protein-ligand interaction information (PLIP) not available DC.14: 5 residues within 4Å: Chain F: R.18, K.21 Chain G: V.47, R.412, N.414 Protein-ligand interaction information (PLIP) not available DC.16: 1 residues within 4Å: Ligands: DC-DA-DA-DA.15 Protein-ligand interaction information (PLIP) not available DC.17: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available DC.18: 2 residues within 4Å: Chain G: R.10, F.277 Protein-ligand interaction information (PLIP) not available DC.19: 4 residues within 4Å: Chain G: K.167 Chain I: Q.35, Q.36 Ligands: DC-DA-DA-DA.15 19 PLIP interactions: 2 interactions with chain I, 2 interactions with chain L, 5 interactions with chain M, 5 interactions with chain J, 2 interactions with chain G, 1 interactions with chain A, 2 interactions with chain O Hydrogen bonds: I:Q.36, L:Q.36, M:K.167, M:D.242, J:K.167, J:D.242, G:K.167, G:D.242, O:Q.36 Salt bridges: I:K.21, L:K.21, M:R.10, M:R.412, J:R.10, J:R.412, A:R.412, O:K.21 Hydrophobic interactions: M:F.277, J:F.277 DC.20: 2 residues within 4Å: Chain G: D.242 Chain I: K.25 Protein-ligand interaction information (PLIP) not available DC.21: 5 residues within 4Å: Chain I: R.18, K.21 Chain J: V.47, R.412, N.414 Protein-ligand interaction information (PLIP) not available DC.23: 1 residues within 4Å: Ligands: DC-DA-DA-DA.22 Protein-ligand interaction information (PLIP) not available DC.24: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available DC.25: 2 residues within 4Å: Chain J: R.10, F.277 Protein-ligand interaction information (PLIP) not available DC.26: 4 residues within 4Å: Chain J: K.167 Chain L: Q.35, Q.36 Ligands: DC-DA-DA-DA.22 Protein-ligand interaction information (PLIP) not available DC.27: 2 residues within 4Å: Chain J: D.242 Chain L: K.25 Protein-ligand interaction information (PLIP) not available DC.28: 5 residues within 4Å: Chain L: R.18, K.21 Chain M: V.47, R.412, N.414 Protein-ligand interaction information (PLIP) not available DC.30: 1 residues within 4Å: Ligands: DC-DA-DA-DA.29 Protein-ligand interaction information (PLIP) not available DC.31: 0 residues within 4Å: (No contacts) Protein-ligand interaction information (PLIP) not available DC.32: 2 residues within 4Å: Chain M: R.10, F.277 Protein-ligand interaction information (PLIP) not available DC.33: 4 residues within 4Å: Chain M: K.167 Chain O: Q.35, Q.36 Ligands: DC-DA-DA-DA.29 Protein-ligand interaction information (PLIP) not available DC.34: 2 residues within 4Å: Chain M: D.242 Chain O: K.25 Protein-ligand interaction information (PLIP) not available DC.35: 5 residues within 4Å: Chain A: V.47, R.412, N.414 Chain O: R.18, K.21 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bernal, R.A. et al., The phiX174 Protein J Mediates DNA Packaging and Viral Attachment to Host Cells. J.Mol.Biol. (2004)

Release Date

2004-04-13

Peptides

Capsid protein: ADGJM
Major spike protein: BEHKN
Small core protein: CFILO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

D
F

G
F

J
F

M
F

B
G

E
G

H
G

K
G

N
G

C
J

F
J

I
J

L
J

O
J

Capsid protein

Major spike protein

Small core protein

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