SMTL ID : 4ytb.1

Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) in complex with dipeptide Asp-Gln.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 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:D.115, A:D.115

1 x ASP: ASPARTIC ACID(Non-covalent)

ASP.2: 4 residues within 4Å: Chain A: W.84, R.111, Y.190 Ligands: GLN.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.111, A:R.111 Water bridges: A:R.109

1 x GLN: GLUTAMINE(Non-covalent)

GLN.3: 11 residues within 4Å: Chain A: W.84, D.87, R.109, R.111, Y.190, I.191, H.193, T.303, D.304, C.308 Ligands: ASP.2 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:W.84, A:W.84, A:I.191 Hydrogen bonds: A:D.87, A:Y.190 Water bridges: A:R.109, A:R.111, A:Y.190 Salt bridges: A:R.109, A:R.111

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: V.183, D.223, M.224, Y.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.223 Water bridges: A:V.182, A:Y.227 GOL.5: 5 residues within 4Å: Chain A: I.106, K.133, N.159, S.161, L.162 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.133, A:N.159 Water bridges: A:K.133, A:K.133, A:S.161 GOL.6: 3 residues within 4Å: Chain A: S.163, Q.164, A.165 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.165 Water bridges: A:S.163, A:S.163, A:Q.164

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 3 residues within 4Å: Chain A: A.347, T.348, N.399 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.348, A:N.399 PO4.8: 3 residues within 4Å: Chain A: P.33, M.34, A.295 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.34 Water bridges: A:E.35, A:S.296, A:T.298 PO4.9: 2 residues within 4Å: Chain A: Q.169, K.172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.169, A:Q.169 Water bridges: A:D.173 Salt bridges: A:K.172 PO4.10: 2 residues within 4Å: Chain A: T.237, K.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.238, A:K.238 PO4.11: 4 residues within 4Å: Chain A: N.385, K.386, N.421, E.422 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.385, A:K.386

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.12: 2 residues within 4Å: Chain A: R.27, P.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.27, A:R.27

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

CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x AZI: AZIDE ION(Non-covalent)

AZI.14: 5 residues within 4Å: Chain A: H.153, Y.156, V.182, V.183, Q.184 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.164

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

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