SMTL ID : 4yt9.1

Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) substrate-unbound.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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:D.104, A:F.105, A:Y.107

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: H.153, Y.156, Q.164, V.182, V.183, Q.184 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.153, A:Q.164, A:V.183 Water bridges: A:Q.164 GOL.3: 5 residues within 4Å: Chain A: V.183, Q.184, D.223, M.224, Y.227 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.184, A:D.223 Water bridges: A:D.181, A:D.181, A:M.224, A:Y.227 GOL.4: 4 residues within 4Å: Chain A: I.106, K.133, N.159, S.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.159 GOL.5: 8 residues within 4Å: Chain A: P.11, V.12, R.13, M.94, Y.95, D.96, T.97, Y.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.11, A:T.97 GOL.6: 6 residues within 4Å: Chain A: K.205, W.235, P.407, D.413, P.414, K.416 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.205, A:K.416, A:K.416 Water bridges: A:N.204, A:K.205, A:D.413, A:D.413 GOL.7: 3 residues within 4Å: Chain A: E.240, V.241, Y.242 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.241, A:V.241 Water bridges: A:E.240, A:E.240, A:E.240, A:Y.242, A:R.243 GOL.8: 9 residues within 4Å: Chain A: Q.184, D.185, P.186, N.192, C.196, W.197, A.220, L.221, M.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.185, A:N.192, A:A.220

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

2015-07-15

Peptides

Peptidylarginine deiminase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptidylarginine deiminase

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