SMTL ID : 6i0x.1 (1 other biounit)

Porphyromonas gingivalis peptidylarginine deminase (PPAD) mutant G231N/E232T/N235D in complex with Cl-amidine.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 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 NA.3: 2 residues within 4Å: Chain A: R.27, D.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.27, A:T.80

1 x BFB: N-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE(Covalent)

BFB.2: 13 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, T.303, D.304, C.308 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.84, A:W.84, A:I.191 Hydrogen bonds: A:D.87, A:D.87, A:R.109, A:R.111, A:R.111, A:Y.190, A:Y.190, A:H.193 Water bridges: A:Y.190, A:T.303

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: N.204, K.205, W.235, E.240, P.407, D.413, P.414, F.415 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.204, A:E.240, A:D.413 Water bridges: A:K.205 GOL.5: 5 residues within 4Å: Chain A: I.106, K.133, N.159, S.161, L.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.159 Water bridges: A:S.161, A:S.161 GOL.6: 5 residues within 4Å: Chain A: V.183, Q.184, D.223, M.224, Y.227 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.184, A:D.223 Water bridges: A:V.182, A:D.223, A:Y.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bereta, G. et al., Structure, function, and inhibition of a genomic/clinical variant of Porphyromonas gingivalis peptidylarginine deiminase. Protein Sci. (2019)

Release Date

2019-01-23

Peptides

Peptidylarginine deiminase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptidylarginine deiminase

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