SMTL ID : 5ak8.1

Structure of C351A mutant of Porphyromonas gingivalis peptidylarginine deiminase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 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(Non-covalent)

ARG.2: 15 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, N.251, T.300, D.301, A.305 Ligands: ALA.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.81, A:W.81, A:I.188 Hydrogen bonds: A:Y.187, A:N.251, A:T.300 Water bridges: A:Y.187 Salt bridges: A:D.84, A:R.106, A:R.108, A:D.192

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

NA.3: 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

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

EDO.4: 6 residues within 4Å: Chain A: Y.15, E.16, D.141, P.200, Y.315, Y.403 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: R.24, S.79, Y.80, W.81 Ligands: EDO.9 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: K.202, E.237, Y.239, T.279, A.280, P.282, D.410 Ligands: EDO.11 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: I.12, E.14, R.83, Y.138, M.139, T.140, E.309 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: K.319, Y.321, E.335, A.336, D.337, H.373 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: R.24, P.26, D.78, Y.80 Ligands: EDO.5 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: I.103, K.130, K.132, N.156, L.159 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: N.201, W.232, P.404, D.410, P.411, F.412 Ligands: EDO.6, EDO.20 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: P.8, R.10, M.91, Y.92, T.94, Y.317 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: 6 residues within 4Å: Chain A: Y.353, Y.376, S.377, F.378, T.379, L.381 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: R.17, R.399, K.400, E.401 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: P.282, P.409, D.410, P.411, K.413 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: A.363, A.364, D.365 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: P.8, V.9, K.169, G.173, T.175 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain A: A.199, N.201, K.202, W.232, P.404, I.406, D.410 Ligands: EDO.11 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: D.182, N.184, G.185, E.186, I.188, N.189 Ligand excluded by PLIP

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