SMTL ID : 5n0m.1

hPAD4 crystal complex with BB-F-amidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: S.409, G.410, R.448 Ligands: 8HT.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.410 Salt bridges: A:R.448 SO4.2: 4 residues within 4Å: Chain A: E.518, K.532, K.534, N.535 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.535 Salt bridges: A:K.532, A:K.534 SO4.9: 4 residues within 4Å: Chain B: S.409, G.410, R.448 Ligands: 8HT.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.410 Salt bridges: B:R.448 SO4.10: 4 residues within 4Å: Chain B: E.518, K.532, K.534, N.535 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.535 Salt bridges: B:K.532, B:K.534

10 x CA: CALCIUM ION(Non-covalent)

CA.3: 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:E.360, A:F.414, A:L.417, H2O.1, H2O.3 CA.4: 4 residues within 4Å: Chain A: E.358, D.376, S.377, N.380 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.358, A:D.376, A:S.377, H2O.2, H2O.3 CA.5: 7 residues within 4Å: Chain A: N.160, D.162, D.164, D.172, D.183, D.186 Ligands: CA.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.162, A:D.172, A:D.183, A:D.186 CA.6: 5 residues within 4Å: Chain A: D.162, D.164, D.186, D.395 Ligands: CA.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.164, A:D.186, A:D.186, A:D.395, H2O.4 CA.7: 4 residues within 4Å: Chain A: D.172, D.175, E.177, D.183 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.172, A:E.177, H2O.2, H2O.3, H2O.6 CA.11: 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:E.360, B:F.414, B:L.417, H2O.8, H2O.10 CA.12: 4 residues within 4Å: Chain B: E.358, D.376, S.377, N.380 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.358, B:D.376, B:S.377, H2O.9, H2O.10 CA.13: 7 residues within 4Å: Chain B: N.160, D.162, D.164, D.172, D.183, D.186 Ligands: CA.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.162, B:D.172, B:D.183, B:D.186 CA.14: 5 residues within 4Å: Chain B: D.162, D.164, D.186, D.395 Ligands: CA.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.164, B:D.186, B:D.186, B:D.395, H2O.10 CA.15: 4 residues within 4Å: Chain B: D.172, D.175, E.177, D.183 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.172, B:E.177, H2O.8, H2O.10, H2O.13

2 x 8HT: ~{N}-[(1~{S})-1-(1~{H}-benzimidazol-2-yl)-4-(2-fluoranylethanimidoylamino)butyl]-4-phenyl-benzamide(Covalent)

8HT.8: 13 residues within 4Å: Chain A: W.354, Q.356, D.357, R.381, G.415, H.478, D.480, I.645, R.646, H.647, G.648, C.652 Ligands: SO4.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.354, A:W.354 Hydrogen bonds: A:D.357, A:H.478, A:D.480, A:R.646 Water bridges: A:R.379 8HT.16: 13 residues within 4Å: Chain B: W.354, Q.356, D.357, R.381, G.415, H.478, D.480, I.645, R.646, H.647, G.648, C.652 Ligands: SO4.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.354, B:W.354 Hydrogen bonds: B:D.357, B:D.480, B:R.646 Water bridges: B:R.379

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muth, A. et al., Development of a Selective Inhibitor of Protein Arginine Deiminase 2. J. Med. Chem. (2017)

Release Date

2017-05-24

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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