SMTL ID : 3b1u.1

Crystal structure of human peptidylarginine deiminase 4 in complex with o-F-amidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x YFF: 2-{[(2S)-1-amino-5-{[(1Z)-2-fluoroethanimidoyl]amino}-1-oxopentan-2-yl]carbamoyl}benzoic acid(Covalent)

YFF.1: 10 residues within 4Å: Chain A: W.355, D.358, R.382, V.477, H.479, D.481, N.596, R.647, H.648, C.653 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.355, A:V.477, A:R.647 Hydrogen bonds: A:R.382, A:R.382, A:H.479, A:D.481, A:R.647, A:H.648 Water bridges: A:S.414, A:S.414, A:R.647, A:R.647, A:R.647 Salt bridges: A:R.382, A:R.647 YFF.10: 10 residues within 4Å: Chain B: W.355, D.358, R.382, V.477, H.479, D.481, N.596, R.647, H.648, C.653 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.355, B:V.477, B:R.647 Hydrogen bonds: B:R.382, B:R.382, B:D.481, B:R.647, B:H.648 Water bridges: B:S.414, B:S.414, B:R.647, B:R.647, B:R.647 Salt bridges: B:R.382, B:R.647

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

SO4.2: 2 residues within 4Å: Chain A: G.411, R.449 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.411 Salt bridges: A:R.449 SO4.3: 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.623, A:K.623 Salt bridges: A:R.503, A:K.507, A:K.623 SO4.4: 2 residues within 4Å: Chain A: K.533, N.536 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.536 Salt bridges: A:K.533 SO4.11: 2 residues within 4Å: Chain B: G.411, R.449 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.411 Salt bridges: B:R.449 SO4.12: 4 residues within 4Å: Chain B: R.503, S.504, K.507, K.623 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.623, B:K.623 Salt bridges: B:R.503, B:K.507, B:K.623 SO4.13: 2 residues within 4Å: Chain B: K.533, N.536 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.536 Salt bridges: B:K.533

10 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.5, H2O.5 CA.6: 4 residues within 4Å: Chain A: E.359, D.377, S.378, N.381 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.359, A:D.377, A:S.378, H2O.5, H2O.6 CA.7: 7 residues within 4Å: Chain A: N.161, D.163, D.165, D.173, D.184, D.187 Ligands: CA.8 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.8: 5 residues within 4Å: Chain A: D.163, D.165, D.187, D.396 Ligands: CA.7 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.4 CA.9: 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.5 CA.14: 5 residues within 4Å: Chain B: Q.357, E.361, F.415, L.418, E.419 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:F.415, B:L.418, B:E.419, H2O.12, H2O.12 CA.15: 4 residues within 4Å: Chain B: E.359, D.377, S.378, N.381 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.359, B:D.377, B:S.378, H2O.12, H2O.13 CA.16: 7 residues within 4Å: Chain B: N.161, D.163, D.165, D.173, D.184, D.187 Ligands: CA.17 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.163, B:D.165, B:D.173, B:D.184, B:D.187 CA.17: 5 residues within 4Å: Chain B: D.163, D.165, D.187, D.396 Ligands: CA.16 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.163, B:D.165, B:D.187, B:D.396, H2O.11 CA.18: 3 residues within 4Å: Chain B: D.173, D.176, E.178 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.173, B:D.176, B:E.178, H2O.11, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Causey, C.P. et al., The Development of N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-fluoro-1-iminoethyl)-l-ornithine Amide (o-F-amidine) and N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-chloro-1-iminoethyl)-l-ornithine Amide (o-Cl-amidine) As Second Generation Protein Arginine Deiminase (PAD) Inhibitors. J.Med.Chem. (2011)

Release Date

2011-10-26

Peptides

Protein-arginine deiminase type-4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein-arginine deiminase type-4

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