SMTL ID : 4ytg.1

Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) mutant C351A in complex with dipeptide Met-Arg.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: D.104, F.105, D.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.105, A:Y.107, A:D.115

1 x CYS: CYSTEINE(Non-covalent)

CYS.2: 7 residues within 4Å: Chain A: Y.335, F.381, T.382, G.383, L.384, F.417, C.419 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:G.383, A:L.384, C.2, C.2

1 x MET: METHIONINE(Non-covalent)

MET.3: 4 residues within 4Å: Chain A: W.84, R.111, Y.190 Ligands: ARG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.111, A:R.111

1 x ARG: ARGININE(Non-covalent)

ARG.4: 16 residues within 4Å: Chain A: W.84, R.86, D.87, R.109, R.111, G.139, Y.190, I.191, H.193, D.195, C.196, N.254, T.303, D.304, A.308 Ligands: MET.3 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:W.84, A:W.84, A:I.191 Hydrogen bonds: A:Y.190, A:N.254, A:T.303 Water bridges: A:R.111, A:Y.190, A:Y.190 Salt bridges: A:D.87, A:R.109, A:R.111, A:D.195

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: I.106, K.133, K.135, N.159, S.161, L.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.159 GOL.6: 4 residues within 4Å: Chain A: V.183, D.223, M.224, Y.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.223 Water bridges: A:D.223 GOL.7: 7 residues within 4Å: Chain A: V.12, R.13, Y.146, G.147, G.176, K.322, Y.324 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.176, A:K.322, A:K.322, A:Y.324 Water bridges: A:G.147, A:Y.324 GOL.8: 8 residues within 4Å: Chain A: N.204, K.205, W.235, E.240, P.407, D.413, F.415 Ligands: AZI.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.204, A:E.240 Water bridges: A:P.414 GOL.9: 6 residues within 4Å: Chain A: Y.356, Y.379, S.380, F.381, T.382, L.384 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.356, A:S.380, A:T.382

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 2 residues within 4Å: Chain A: T.5, N.6 Ligand excluded by PLIP

2 x AZI: AZIDE ION(Non-covalent)

AZI.11: 3 residues within 4Å: Chain A: G.188, E.189, N.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.188, A:N.192, A:N.192 AZI.12: 5 residues within 4Å: Chain A: K.205, E.240, Y.242, D.413 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.205, A:D.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goulas, T. et al., Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase. Sci Rep (2015)

Release Date

2015-07-01

Peptides

Peptidylarginine deiminase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptidylarginine deiminase