SMTL ID : 4rdb.1

Crystal structure of an immunoreactive 32 kDa antigen PG49 (PG_0181) from Porphyromonas gingivalis W83 at 1.45 A resolution (PSI Community Target, Nakayama)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: W.120, S.121, F.182, Y.184, S.206, T.218 Ligands: ACN.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.206, A:S.206, A:T.218 Water bridges: A:S.121, A:T.218 EDO.2: 4 residues within 4Å: Chain A: N.49, M.76, E.80, R.84 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.49, A:E.80, A:E.80, A:R.84, A:R.84 EDO.3: 7 residues within 4Å: Chain A: K.52, Y.53, Y.54, F.60, T.61 Ligands: EDO.8, EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.52, A:Y.54 Water bridges: A:T.61 EDO.4: 6 residues within 4Å: Chain A: F.166, E.283, L.284, Y.285, I.305 Ligands: EDO.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.283 Water bridges: A:K.165, A:L.284, A:L.284 EDO.5: 1 residues within 4Å: Chain A: T.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.226, A:T.226 EDO.6: 6 residues within 4Å: Chain A: R.114, D.123, I.124, A.125, P.127, F.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.123, A:A.125, A:P.127 Water bridges: A:R.114 EDO.7: 6 residues within 4Å: Chain A: D.44, Q.45, E.80, A.81, E.83, R.84 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.45, A:E.83 Water bridges: A:E.80, A:E.83, A:E.83, A:R.84 EDO.8: 6 residues within 4Å: Chain A: Y.39, K.52, Y.54, K.97, D.101 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.97, A:K.97 EDO.9: 7 residues within 4Å: Chain A: Y.54, I.55, T.56, G.57, T.59, F.60 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.56, A:G.57, A:T.59 EDO.10: 4 residues within 4Å: Chain A: T.111, K.113, Y.192, P.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.111, A:Y.192 EDO.11: 5 residues within 4Å: Chain A: V.169, P.170, I.172, L.238, G.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.242 EDO.12: 4 residues within 4Å: Chain A: L.284, Y.285, R.286 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.286 EDO.13: 4 residues within 4Å: Chain A: R.10, D.12, D.13, R.25 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.10, A:D.12, A:D.12, A:D.13, A:D.13

1 x ACN: ACETONE(Non-covalent)

ACN.14: 7 residues within 4Å: Chain A: S.121, F.182, Y.184, G.233, V.250, T.251 Ligands: EDO.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.182 Hydrogen bonds: A:Y.184 Water bridges: A:T.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Q. et al., A Distinct Type of Pilus from the Human Microbiome. Cell (2016)

Release Date

2014-12-03

Peptides

Immunoreactive 32 kDa antigen PG49: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Immunoreactive 32 kDa antigen PG49