SMTL ID : 3n9r.3 (3 other biounits)

Class II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex with N-(4-hydroxybutyl)-phosphoglycolohydroxamic acid, a competitive inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.83, H.180, H.210, G.211, N.253 Ligands: TD3.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.83, A:H.180, A:H.210 ZN.5: 6 residues within 4Å: Chain B: H.83, H.180, H.210, G.211, N.253 Ligands: TD3.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.83, B:H.180, B:H.210

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

NA.2: 10 residues within 4Å: Chain A: Q.47, H.80, D.82, H.83, M.102, E.132, V.208, H.210, K.251, N.253 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.80, A:E.132, A:H.210, A:K.251, A:N.253 NA.6: 9 residues within 4Å: Chain B: Q.47, H.80, D.82, H.83, M.102, E.132, H.210, K.251, N.253 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.47, B:H.80, B:H.210, B:K.251, B:N.253

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

CL.3: 4 residues within 4Å: Chain A: H.83, D.104, S.106, E.134 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: D.104, S.106, E.134 Ligand excluded by PLIP

2 x TD3: 2-[hydroxy(4-hydroxybutyl)amino]-2-oxoethyl dihydrogen phosphate(Non-covalent)

TD3.4: 15 residues within 4Å: Chain A: D.82, H.83, H.180, G.181, K.184, H.210, G.211, A.212, S.213, N.253, T.254, D.255, T.256, D.257 Ligands: ZN.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.181, A:G.181, A:G.211, A:G.211, A:A.212, A:S.213, A:N.253, A:D.255, A:T.256 Water bridges: A:N.23, A:R.259 Salt bridges: A:K.184 TD3.8: 15 residues within 4Å: Chain B: N.23, D.82, H.83, H.180, G.181, K.184, H.210, G.211, A.212, S.213, N.253, T.254, D.255, T.256 Ligands: ZN.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.181, B:G.181, B:G.211, B:G.211, B:A.212, B:S.213, B:N.253, B:D.255, B:T.256, B:T.256 Water bridges: B:N.23, B:D.255, B:T.256, B:T.256 Salt bridges: B:K.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Daher, R. et al., Rational Design, Synthesis, and Evaluation of New Selective Inhibitors of Microbial Class II (Zinc Dependent) Fructose Bis-phosphate Aldolases. J.Med.Chem. (2010)

Release Date

2010-11-17

Peptides

Fructose-bisphosphate aldolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
Z

Fructose-bisphosphate aldolase

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