SMTL ID : 1wda.1

Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with benzoyl-L-arginine amide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: Q.356, E.360, F.414, L.417, E.418 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.414, A:L.417, A:E.418, H2O.1, H2O.2 CA.2: 7 residues within 4Å: Chain A: N.160, D.162, D.164, D.172, D.183, D.186 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.162, A:D.164, A:D.172, A:D.183, A:D.186 CA.3: 5 residues within 4Å: Chain A: D.162, D.164, D.186, D.395 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.162, A:D.164, A:D.164, A:D.186, A:D.395 CA.4: 4 residues within 4Å: Chain A: E.358, D.376, S.377, N.380 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.358, A:D.376, A:S.377, H2O.7 CA.5: 3 residues within 4Å: Chain A: D.172, D.175, E.177 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.172, A:D.175, A:E.177, H2O.6, H2O.7 CA.10: 5 residues within 4Å: Chain B: Q.356, E.360, F.414, L.417, E.418 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:F.414, B:L.417, B:E.418, H2O.7, H2O.8 CA.11: 7 residues within 4Å: Chain B: N.160, D.162, D.164, D.172, D.183, D.186 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.162, B:D.164, B:D.172, B:D.183, B:D.186 CA.12: 5 residues within 4Å: Chain B: D.162, D.164, D.186, D.395 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.162, B:D.164, B:D.164, B:D.186, B:D.395 CA.13: 4 residues within 4Å: Chain B: E.358, D.376, S.377, N.380 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.358, B:D.376, B:S.377, H2O.13 CA.14: 3 residues within 4Å: Chain B: D.172, D.175, E.177 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.172, B:D.175, B:E.177, H2O.12, H2O.13

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

SO4.6: 3 residues within 4Å: Chain A: S.409, G.410, R.448 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.410 Salt bridges: A:R.448 SO4.7: 4 residues within 4Å: Chain A: R.502, S.503, K.506, K.622 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.503 Salt bridges: A:R.502, A:K.506, A:K.622 SO4.8: 3 residues within 4Å: Chain A: E.518, K.532, N.535 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.535 Salt bridges: A:K.532 SO4.15: 3 residues within 4Å: Chain B: S.409, G.410, R.448 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.410 Salt bridges: B:R.448 SO4.16: 4 residues within 4Å: Chain B: R.502, S.503, K.506, K.622 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.503 Salt bridges: B:R.502, B:K.506, B:K.622 SO4.17: 3 residues within 4Å: Chain B: E.518, K.532, N.535 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.535 Salt bridges: B:K.532

2 x BAG: N-[(E)-2-AMINO-1-(3-{[AMINO(IMINO)METHYL]AMINO}PROPYL)-2-HYDROXYVINYL]BENZAMIDE(Non-covalent)

BAG.9: 13 residues within 4Å: Chain A: W.354, Q.356, D.357, R.381, G.415, V.476, H.478, D.480, E.481, N.595, R.646, H.647, A.652 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.354, A:V.476, A:R.646 Hydrogen bonds: A:D.357, A:D.357, A:R.381, A:R.381, A:H.478, A:N.595, A:R.646 Water bridges: A:E.481 Salt bridges: A:D.357, A:D.480 BAG.18: 13 residues within 4Å: Chain B: W.354, Q.356, D.357, R.381, G.415, V.476, H.478, D.480, E.481, N.595, R.646, H.647, A.652 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.354, B:V.476, B:R.646 Hydrogen bonds: B:D.357, B:R.381, B:R.381, B:N.595, B:R.646 Water bridges: B:E.481 Salt bridges: B:D.357, B:D.480

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arita, K. et al., Structural basis for Ca(2+)-induced activation of human PAD4. Nat.Struct.Mol.Biol. (2004)

Release Date

2004-07-13

Peptides

Protein-arginine deiminase type IV: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein-arginine deiminase type IV

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