SMTL ID : 4dkt.1

Crystal structure of human peptidylarginine deiminase 4 in complex with N-acetyl-L-threonyl-L-alpha-aspartyl-N5-[(1E)-2-fluoroethanimidoyl]-L-ornithinamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

homo-dimer

Ligands

2 x ASP- FIO- NH2: Thr-Asp-F-amidine(Non-covalent)

ASP-FIO-NH2.1: 14 residues within 4Å: Chain A: Q.351, W.352, D.355, R.377, R.379, V.474, H.476, D.478, N.593, R.644, H.645, G.646, E.647, C.650 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.474, A:R.644 Hydrogen bonds: A:Q.351, A:W.352, A:D.355, A:R.377, A:R.379, A:R.379, A:H.476, A:N.593, A:R.644, A:R.644 Salt bridges: A:R.644 ASP-FIO-NH2.11: 14 residues within 4Å: Chain B: Q.351, W.352, D.355, R.377, R.379, V.474, H.476, D.478, N.593, R.644, H.645, G.646, E.647, C.650 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.474, B:R.644 Hydrogen bonds: B:Q.351, B:D.355, B:R.377, B:R.379, B:R.379, B:H.476, B:H.476, B:N.593, B:R.644 Salt bridges: B:R.644

10 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: Q.354, E.358, F.412, L.415, E.416 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.358, A:F.412, A:L.415, A:E.416 CA.3: 7 residues within 4Å: Chain A: N.158, D.160, D.162, D.170, D.181, D.184 Ligands: CA.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.160, A:D.162, A:D.170, A:D.181, A:D.184 CA.4: 6 residues within 4Å: Chain A: D.160, D.162, E.180, D.184, D.393 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.160, A:D.162, A:D.184, A:D.184, A:D.393 CA.5: 5 residues within 4Å: Chain A: E.356, D.374, S.375, N.378, Q.402 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.356, A:D.374, A:D.374, A:S.375 CA.6: 6 residues within 4Å: Chain A: D.170, D.173, E.175, D.181, M.185, E.257 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.173, A:D.181 CA.12: 5 residues within 4Å: Chain B: Q.354, E.358, F.412, L.415, E.416 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.358, B:F.412, B:L.415, B:E.416 CA.13: 7 residues within 4Å: Chain B: N.158, D.160, D.162, D.170, D.181, D.184 Ligands: CA.14 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.160, B:D.162, B:D.170, B:D.181, B:D.184 CA.14: 6 residues within 4Å: Chain B: D.160, D.162, E.180, D.184, D.393 Ligands: CA.13 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.160, B:D.162, B:D.184, B:D.184, B:D.393 CA.15: 5 residues within 4Å: Chain B: E.356, D.374, S.375, N.378, Q.402 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.356, B:D.374, B:D.374, B:S.375 CA.16: 6 residues within 4Å: Chain B: D.170, D.173, E.175, D.181, M.185, E.257 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.173, B:D.181

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

SO4.7: 3 residues within 4Å: Chain A: S.407, G.408, R.446 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.407, A:G.408 Salt bridges: A:R.446 SO4.8: 3 residues within 4Å: Chain A: K.530, K.532, N.533 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.533 Salt bridges: A:K.530, A:K.532 SO4.17: 3 residues within 4Å: Chain B: S.407, G.408, R.446 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.407, B:G.408 Salt bridges: B:R.446 SO4.18: 3 residues within 4Å: Chain B: K.530, K.532, N.533 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.533 Salt bridges: B:K.530, B:K.532

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 4 residues within 4Å: Chain A: R.541, N.544, S.545, E.548 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.544 EDO.10: 7 residues within 4Å: Chain A: D.437, S.438, C.439, K.466, L.467, Y.468, W.553 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.437, A:W.553 EDO.19: 4 residues within 4Å: Chain B: R.541, N.544, S.545, E.548 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.544 EDO.20: 7 residues within 4Å: Chain B: D.437, S.438, C.439, K.466, L.467, Y.468, W.553 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.437, B:D.437, B:W.553

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, J.E. et al., Synthesis and Screening of a Haloacetamidine Containing Library To Identify PAD4 Selective Inhibitors. Acs Chem.Biol. (2012)

Release Date

2012-02-29

Peptides

Protein-arginine deiminase type-4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein-arginine deiminase type-4