SMTL ID : 2dew.1

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal tail including Arg8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: Q.357, E.361, F.415, L.418, E.419 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.415, A:L.418, A:E.419, H2O.1, H2O.1 CA.2: 7 residues within 4Å: Chain A: N.161, D.163, D.165, D.173, D.184, D.187 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.163, A:D.165, A:D.173, A:D.184, A:D.187 CA.3: 5 residues within 4Å: Chain A: D.163, D.165, D.187, D.396 Ligands: CA.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.163, A:D.165, A:D.187, A:D.396, H2O.5 CA.4: 4 residues within 4Å: Chain A: E.359, D.377, S.378, N.381 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.359, A:D.377, A:S.378, H2O.6 CA.5: 3 residues within 4Å: Chain A: D.173, D.176, E.178 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.173, A:D.176, A:E.178, H2O.4, H2O.4 CA.9: 5 residues within 4Å: Chain C: Q.357, E.361, F.415, L.418, E.419 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:F.415, C:L.418, C:E.419, H2O.9, H2O.10 CA.10: 7 residues within 4Å: Chain C: N.161, D.163, D.165, D.173, D.184, D.187 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.163, C:D.165, C:D.173, C:D.184, C:D.187 CA.11: 5 residues within 4Å: Chain C: D.163, D.165, D.187, D.396 Ligands: CA.10 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.163, C:D.165, C:D.187, C:D.396, H2O.13 CA.12: 4 residues within 4Å: Chain C: E.359, D.377, S.378, N.381 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.359, C:D.377, C:S.378, H2O.15 CA.13: 3 residues within 4Å: Chain C: D.173, D.176, E.178 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.173, C:D.176, C:E.178, H2O.12, H2O.13

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 5 residues within 4Å: Chain A: S.410, G.411, R.449 Chain B: K.6, S.7 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.411 Water bridges: A:G.411, A:V.477 Salt bridges: A:R.449, B:K.6 SO4.7: 4 residues within 4Å: Chain A: R.503, S.504, K.507, K.623 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.507, A:K.507 Salt bridges: A:R.503, A:K.507, A:K.623 SO4.8: 4 residues within 4Å: Chain A: E.519, K.533, K.535, N.536 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.536 Salt bridges: A:K.533, A:K.535 SO4.14: 5 residues within 4Å: Chain C: S.410, G.411, R.449 Chain D: K.6, S.7 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Salt bridges: D:K.6, C:R.449 Hydrogen bonds: C:G.411 Water bridges: C:G.411, C:V.477 SO4.15: 4 residues within 4Å: Chain C: R.503, S.504, K.507, K.623 5 PLIP interactions: 5 interactions with chain C Water bridges: C:K.507, C:K.507 Salt bridges: C:R.503, C:K.507, C:K.623 SO4.16: 4 residues within 4Å: Chain C: E.519, K.533, K.535, N.536 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.536 Salt bridges: C:K.533, C:K.535

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arita, K. et al., Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-04-11

Peptides

Protein-arginine deiminase type IV: AC
10-mer peptide from histone H3: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

C
X

B
A

D
A

Protein-arginine deiminase type IV

10-mer peptide from histone H3

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