SMTL ID : 5ak7.1

Structure of wt Porphyromonas gingivalis peptidylarginine deiminase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

monomer

Ligands

1 x ALA: ALANINE(Non-covalent)

ALA.1: 4 residues within 4Å: Chain A: W.81, R.108, Y.187 Ligands: ARG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.108, A:R.108

1 x ARG: ARGININE(Covalent)

ARG.2: 14 residues within 4Å: Chain A: W.81, R.83, D.84, R.106, R.108, G.136, Y.187, I.188, H.190, D.192, T.300, D.301, C.305 Ligands: ALA.1 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:W.81, A:W.81, A:I.188 Hydrogen bonds: A:D.84, A:D.84, A:Y.187 Water bridges: A:Y.104, A:R.106, A:Y.187, A:T.300 Salt bridges: A:R.106, A:R.108

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

EDO.3: 5 residues within 4Å: Chain A: R.24, S.79, Y.80, W.81 Ligands: EDO.17 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: Y.15, E.16, D.141, Y.143, P.200, Y.315, Y.403 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: K.202, E.237, Y.239, T.279, A.280, P.282, D.410 Ligands: EDO.6 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: N.201, W.232, P.404, D.410, P.411, F.412 Ligands: EDO.5 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: K.319, Y.321, E.335, A.336, D.337, H.373 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: I.103, K.130, N.156, S.158, L.159 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: Y.353, Y.376, S.377, F.378, T.379, L.381 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: P.8, R.10, M.91, Y.92, D.93, T.94 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: P.282, P.409, D.410, P.411, K.413 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: K.130, K.167 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: V.180, D.220, M.221, Y.224 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: D.141, S.145, Q.228, T.229, C.230, A.231, Y.236 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: D.71, F.72, Y.121 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: N.165, T.175, H.176, H.177 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: R.24, D.78, Y.80 Ligands: EDO.3 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: E.237, V.238, Y.239 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: S.157, S.158, L.159, S.160 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.20: 3 residues within 4Å: Chain A: D.101, F.102, D.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.102, A:D.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Montgomery, A.B. et al., Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase: Implications for Autoimmunity in Rheumatoid Arthritis. Ann.Rheum.Dis. (2016)

Release Date

2015-07-22

Peptides

PEPTIDYLARGININE DEIMINASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PEPTIDYLARGININE DEIMINASE