SMTL ID : 2dw5.1

Crystal structure of human peptidylarginine deiminase 4 in complex with N-alpha-benzoyl-N5-(2-fluoro-1-iminoethyl)-L-ornithine 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.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.11, H2O.32 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: 5 interactions with chain A Metal complexes: A:D.165, A:D.165, A:D.187, A:D.187, A:D.396 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.128 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.124, H2O.129 CA.10: 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.161, H2O.182 CA.11: 7 residues within 4Å: Chain B: N.161, D.163, D.165, D.173, D.184, D.187 Ligands: CA.12 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.12: 5 residues within 4Å: Chain B: D.163, D.165, D.187, D.396 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.165, B:D.165, B:D.187, B:D.187, B:D.396 CA.13: 4 residues within 4Å: Chain B: E.359, D.377, S.378, N.381 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.359, B:D.377, B:S.378, H2O.278 CA.14: 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.274, H2O.279

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

SO4.6: 3 residues within 4Å: Chain A: S.410, G.411, R.449 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.411 Salt bridges: A:R.449 SO4.7: 4 residues within 4Å: Chain A: R.503, S.504, K.507, K.623 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.504 Salt bridges: A:R.503, A:K.507, A:K.623 SO4.8: 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 SO4.15: 3 residues within 4Å: Chain B: S.410, G.411, R.449 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.411 Salt bridges: B:R.449 SO4.16: 4 residues within 4Å: Chain B: R.503, S.504, K.507, K.623 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.504 Salt bridges: B:R.503, B:K.507, B:K.623 SO4.17: 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

2 x BFB: N-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE(Covalent)

BFB.9: 11 residues within 4Å: Chain A: W.355, D.358, R.382, G.416, V.477, H.479, D.481, N.596, R.647, H.648, C.653 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.355, A:V.477, A:R.647, A:R.647 Hydrogen bonds: A:D.358, A:R.382, A:R.382, A:R.647 Water bridges: A:S.414 BFB.18: 11 residues within 4Å: Chain B: W.355, D.358, R.382, G.416, V.477, H.479, D.481, N.596, R.647, H.648, C.653 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.355, B:V.477, B:R.647, B:R.647 Hydrogen bonds: B:D.358, B:R.382, B:R.382, B:H.479, B:R.647 Water bridges: B:S.414

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, Y. et al., Inhibitors and Inactivators of Protein Arginine Deiminase 4: Functional and Structural Characterization. Biochemistry (2006)

Release Date

2006-10-17

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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