SMTL ID : 4x8g.1

Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with GSK199

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.29 Å

Oligo State

homo-dimer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.361, F.415, L.418, E.419 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.361, A:F.415, A:L.418, A:E.419, H2O.1 CA.2: 6 residues within 4Å: Chain A: N.161, D.163, D.165, D.173, D.184, D.187 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, K.370, D.396 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.165, A:D.187, A:D.187, A:D.396 CA.4: 3 residues within 4Å: Chain A: D.173, D.176, E.178 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.173, A:D.176, H2O.1, H2O.1, H2O.1 CA.6: 4 residues within 4Å: Chain B: E.361, F.415, L.418, E.419 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.361, B:F.415, B:L.418, B:E.419, H2O.2 CA.7: 6 residues within 4Å: Chain B: N.161, D.163, D.165, D.173, D.184, D.187 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.8: 5 residues within 4Å: Chain B: D.163, D.165, D.187, K.370, D.396 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.165, B:D.187, B:D.187, B:D.396 CA.9: 3 residues within 4Å: Chain B: D.173, D.176, E.178 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.173, B:D.176, H2O.2, H2O.2, H2O.2

2 x 3Z0: [(3R)-3-aminopiperidin-1-yl][2-(1-ethyl-1H-pyrrolo[2,3-b]pyridin-2-yl)-7-methoxy-1-methyl-1H-benzimidazol-5-yl]methanone(Non-covalent)

3Z0.5: 13 residues within 4Å: Chain A: G.416, V.477, H.479, D.481, E.482, A.589, F.590, F.591, P.592, N.593, N.596, F.642, V.651 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.592, A:N.593, A:F.642 Hydrogen bonds: A:D.481, A:N.593, A:N.593, A:N.596 pi-Stacking: A:F.642 3Z0.10: 13 residues within 4Å: Chain B: G.416, V.477, H.479, D.481, E.482, A.589, F.590, F.591, P.592, N.593, N.596, F.642, V.651 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.592, B:N.593, B:F.642 Hydrogen bonds: B:H.479, B:D.481, B:N.593, B:N.593, B:N.596 pi-Stacking: B:F.642

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lewis, H.D. et al., Inhibition of PAD4 activity is sufficient to disrupt mouse and human NET formation. Nat.Chem.Biol. (2015)

Release Date

2015-01-28

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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