SMTL ID : 3n9s.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x TD4: 4-{hydroxy[(phosphonooxy)acetyl]amino}butyl dihydrogen phosphate(Non-covalent)

TD4.1: 21 residues within 4Å: Chain A: N.23, Q.47, S.49, G.51, A.52, 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 Chain B: R.280 Ligands: ZN.2 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.49, A:S.49, A:G.181, A:G.211, A:G.211, A:A.212, A:S.213, A:N.253, A:D.255, A:T.256, A:T.256 Water bridges: A:E.50, A:D.255, B:R.280, B:R.280 Salt bridges: A:K.184, B:R.280 TD4.8: 21 residues within 4Å: Chain A: R.280 Chain B: N.23, Q.47, S.49, G.51, A.52, 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.5 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.47, B:S.49, B:S.49, B:A.52, 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:E.50, B:R.259, B:R.259, B:R.259 Salt bridges: B:K.184, A:R.280

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.83, L.138, H.180, H.210, N.253 Ligands: TD4.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.83, A:H.180, A:H.210 ZN.5: 5 residues within 4Å: Chain B: H.83, H.180, H.210, N.253 Ligands: TD4.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.83, B:H.180, B:H.210

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: H.83, D.104, S.106, E.134 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.104, A:E.134, H2O.1, H2O.6, H2O.13 CA.6: 3 residues within 4Å: Chain B: D.104, S.106, E.134 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.104, B:E.134, H2O.25, H2O.25, H2O.28

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

NA.4: 9 residues within 4Å: Chain A: Q.47, H.80, D.82, H.83, M.102, E.132, H.210, K.251, N.253 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.80, A:D.82, A:D.82, A:H.210, A:K.251, A:N.253 NA.7: 9 residues within 4Å: Chain B: Q.47, H.80, D.82, H.83, M.102, E.132, H.210, K.251, N.253 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.80, B:E.132, B:K.251, B:N.253

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
A

B
B

Fructose-bisphosphate aldolase

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