SMTL ID : 5vjf.1

Class II fructose-1,6-bisphosphate aldolase of Helicobacter pylori with DHAP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.83, H.180, H.210 Ligands: 13P.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.83, A:H.180, A:H.210, H2O.1 ZN.6: 4 residues within 4Å: Chain B: H.83, H.180, H.210 Ligands: 13P.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.83, B:H.180, B:H.210, H2O.18

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

NA.2: 9 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:H.80, A:E.132, 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.80, B:D.82, B:D.82, B:H.210, B:K.251, B:N.253

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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.104, A:D.104, A:S.106, A:E.134, H2O.10 CA.8: 4 residues within 4Å: Chain B: H.83, D.104, S.106, E.134 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.104, B:S.106, B:E.134, H2O.24, H2O.26

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Chain A: G.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.232

2 x 13P: 1,3-DIHYDROXYACETONEPHOSPHATE(Non-covalent)

13P.5: 17 residues within 4Å: Chain A: N.23, Q.47, 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 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Q.47, A:D.82, A:G.181, A:G.211, A:A.212, A:S.213, A:S.213, A:N.253, A:D.255, A:T.256, A:T.256, A:T.256 Water bridges: A:N.23, A:H.180, A:H.180 Salt bridges: A:K.184 13P.9: 17 residues within 4Å: Chain B: N.23, Q.47, 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.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.47, B:D.82, B:G.181, B:G.211, B:A.212, B:S.213, B:S.213, B:N.253, B:D.255, B:T.256, B:T.256, B:T.256 Water bridges: B:H.180, B:D.255 Salt bridges: B:K.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jacques, B. et al., Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases. J. Biol. Chem. (2018)

Release Date

2018-04-11

Peptides

Fructose-bisphosphate aldolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fructose-bisphosphate aldolase

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