SMTL ID : 5oey.1

Crystal structure of Leishmania major fructose-1,6-bisphosphatase in holo form.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 12 residues within 4Å: Chain A: D.68, E.97, D.118, L.120, D.121, G.122, S.123, R.280, E.284 Ligands: MN.2, MN.3, K.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.122 Salt bridges: A:R.280 PO4.5: 10 residues within 4Å: Chain B: E.97, D.118, L.120, D.121, G.122, S.123, E.284 Ligands: MN.6, MN.7, K.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.120, B:G.122, B:S.123 PO4.9: 12 residues within 4Å: Chain C: D.68, E.97, D.118, L.120, D.121, G.122, S.123, R.280, E.284 Ligands: MN.10, MN.11, K.12 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.122, C:S.123 Water bridges: C:L.120 Salt bridges: C:R.280 PO4.14: 11 residues within 4Å: Chain D: D.74, E.97, D.118, L.120, D.121, G.122, S.123, E.284 Ligands: MN.15, MN.16, K.17 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.121, D:D.121, D:G.122, D:S.123

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 8 residues within 4Å: Chain A: D.74, E.97, E.98, D.118, L.120, D.121 Ligands: PO4.1, K.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.97, A:D.118, A:L.120 MN.3: 4 residues within 4Å: Chain A: D.118, D.121, E.284 Ligands: PO4.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.118, A:D.121, A:E.284 MN.6: 8 residues within 4Å: Chain B: D.74, E.97, E.98, D.118, L.120, D.121 Ligands: PO4.5, MN.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.97, B:D.118, B:L.120, H2O.1 MN.7: 6 residues within 4Å: Chain B: E.97, D.118, D.121, E.284 Ligands: PO4.5, MN.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.97, B:D.118, B:E.284 MN.10: 8 residues within 4Å: Chain C: E.97, E.98, D.118, L.120, D.121 Ligands: PO4.9, MN.11, K.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.97, C:D.118, C:D.118, C:L.120, H2O.3 MN.11: 5 residues within 4Å: Chain C: D.118, D.121, E.284 Ligands: PO4.9, MN.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.118, C:D.121, C:E.284 MN.15: 4 residues within 4Å: Chain D: D.74, E.98 Ligands: PO4.14, K.17 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.74, D:E.98, D:E.98 MN.16: 6 residues within 4Å: Chain D: E.97, D.118, D.121, E.284 Ligands: PO4.14, K.17 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.97, D:E.97, D:D.118, D:D.121, D:E.284

4 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: D.68, E.97 Ligands: PO4.1, MN.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.68, A:E.97 K.8: 2 residues within 4Å: Chain B: K.278 Ligands: PO4.5 No protein-ligand interaction detected (PLIP) K.12: 5 residues within 4Å: Chain C: D.68, E.97, S.123 Ligands: PO4.9, MN.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.68, C:E.97 K.17: 8 residues within 4Å: Chain D: D.74, E.97, E.98, D.118, L.120 Ligands: PO4.14, MN.15, MN.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.97, D:E.98, D:D.118, D:L.120

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.13: 3 residues within 4Å: Chain A: K.52 Chain C: R.48, K.52 5 PLIP interactions: 5 interactions with chain C Water bridges: C:K.44, C:K.44 Salt bridges: C:K.44, C:R.48, C:K.52 CIT.18: 3 residues within 4Å: Chain B: K.52 Chain D: K.44, K.52 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:K.52, B:K.52 Salt bridges: D:K.44, D:K.52, B:K.44, B:K.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, M. et al., Structures of Leishmania Fructose-1,6-Bisphosphatase Reveal Species-Specific Differences in the Mechanism of Allosteric Inhibition. J. Mol. Biol. (2017)

Release Date

2017-09-20

Peptides

FBP protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

FBP protein

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