SMTL ID : 3mjf.1

Phosphoribosylamine-glycine ligase from Yersinia pestis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: E.196, E.197, Q.216, D.217, H.218, D.225, R.419, Y.424, R.425 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.197, A:R.419, A:R.419, A:Y.424, A:R.425 Water bridges: A:K.219, A:K.219 GOL.2: 4 residues within 4Å: Chain A: Q.401, Q.402, Y.405, K.420 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.420 Water bridges: A:Q.402

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 4 residues within 4Å: Chain A: Q.99, A.100, Q.103, N.267 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.100, A:A.100

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: E.165, E.168, T.169, N.172, D.173 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.172, A:D.173

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

EDO.5: 5 residues within 4Å: Chain A: A.213, P.238, R.305, W.329 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.305, A:R.305

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.6: 3 residues within 4Å: Chain A: L.339, V.416, C.418 No protein-ligand interaction detected (PLIP)

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 2 residues within 4Å: Chain A: Y.344, R.386 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.344, A:R.386 Water bridges: A:Y.348, A:G.385, A:G.385, A:G.385, A:G.385, A:G.385, A:R.386 Salt bridges: A:R.386 SO4.8: 5 residues within 4Å: Chain A: A.213, T.214, P.238, V.242 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.214, A:H.247 SO4.9: 3 residues within 4Å: Chain A: A.264, E.265, G.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.265 SO4.10: 5 residues within 4Å: Chain A: A.153, G.155, K.156, G.157, V.158 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.155, A:K.156, A:G.157, A:V.158 Water bridges: A:A.149, A:D.150, A:N.229 SO4.11: 4 residues within 4Å: Chain A: G.106, S.107, K.108, A.109 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.108, A:A.109 Water bridges: A:K.108, A:K.108 Salt bridges: A:K.108

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

NA.12: 8 residues within 4Å: Chain A: D.217, K.219, G.231, G.232, R.293, D.296, P.297, E.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.296, A:E.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., X-ray crystal structure of phosphoribosylamine-glycine ligase from Yersinia pestis. To be Published

Release Date

2010-05-26

Peptides

Phosphoribosylamine--glycine ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoribosylamine--glycine ligase