SMTL ID : 5n1b.1

hPAD4 crystal complex with AFM-14a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 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: 8FW.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.410 Salt bridges: A:R.448 SO4.2: 2 residues within 4Å: Chain A: K.532, N.535 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.535 Salt bridges: A:K.532 SO4.9: 4 residues within 4Å: Chain B: S.409, G.410, R.448 Ligands: 8FW.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.410 Salt bridges: B:R.448 SO4.10: 2 residues within 4Å: Chain B: K.532, N.535 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.535 Salt bridges: B:K.532

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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.360, A:F.414, A:L.417, A:E.418, H2O.1 CA.4: 4 residues within 4Å: Chain A: E.358, D.376, S.377, N.380 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.358, A:D.376, A:S.377 CA.5: 7 residues within 4Å: Chain A: N.160, D.162, D.164, D.172, D.183, D.186 Ligands: CA.6 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.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.162, A:D.164, A:D.186, A:D.395, H2O.4 CA.7: 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.1, H2O.2 CA.11: 5 residues within 4Å: Chain B: Q.356, E.360, F.414, L.417, E.418 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.360, B:F.414, B:L.417, B:E.418, H2O.8 CA.12: 4 residues within 4Å: Chain B: E.358, D.376, S.377, N.380 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.358, B:D.376, B:S.377 CA.13: 7 residues within 4Å: Chain B: N.160, D.162, D.164, D.172, D.183, D.186 Ligands: CA.14 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.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.162, B:D.164, B:D.186, B:D.395, H2O.11 CA.15: 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.8, H2O.9

2 x 8FW: ~{N}-[(1~{S})-1-(1~{H}-benzimidazol-2-yl)-4-(ethanimidoylamino)butyl]-3-oxidanylidene-isoindole-4-carboxamide(Covalent)

8FW.8: 12 residues within 4Å: Chain A: W.354, D.357, R.381, G.415, V.476, H.478, D.480, N.595, R.646, H.647, C.652 Ligands: SO4.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.354 Hydrogen bonds: A:R.381, A:H.478, A:D.480, A:R.646 Water bridges: A:S.413, A:H.647 8FW.16: 12 residues within 4Å: Chain B: W.354, D.357, R.381, G.415, V.476, H.478, D.480, N.595, R.646, H.647, C.652 Ligands: SO4.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.354 Hydrogen bonds: B:R.381, B:H.478, B:D.480, B:R.646 Water bridges: B:S.413

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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