SMTL ID : 5tlh.1

Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor 2-naphthol 6-bisphosphonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x RD2: [(6-hydroxynaphthalen-2-yl)methylene]bis(phosphonic acid)(Non-covalent)

RD2.1: 9 residues within 4Å: Chain A: E.34, R.42, S.45, G.302, R.303, Q.306, A.307, L.310, K.311 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.42, A:R.303, A:R.303 Hydrogen bonds: A:R.42, A:R.42, A:R.303, A:R.303, A:K.311 Water bridges: A:G.302 pi-Cation interactions: A:R.42 RD2.4: 10 residues within 4Å: Chain B: E.34, R.42, S.45, Y.58, G.302, R.303, Q.306, A.307, L.310, K.311 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.42, B:R.303, B:R.303, B:R.303 Hydrogen bonds: B:R.42, B:K.311 Water bridges: B:G.302 RD2.6: 9 residues within 4Å: Chain C: E.34, R.42, S.45, G.302, R.303, Q.306, A.307, L.310, K.311 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:R.303, C:R.303 Hydrogen bonds: C:E.34, C:R.42, C:R.42, C:R.303, C:R.303, C:K.311 Water bridges: C:S.45, C:S.45 pi-Cation interactions: C:R.42 RD2.9: 11 residues within 4Å: Chain D: A.31, E.34, R.42, S.45, Y.58, G.302, R.303, Q.306, A.307, L.310, K.311 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:R.303, D:R.303 Hydrogen bonds: D:E.34, D:E.34, D:R.42, D:R.42, D:K.311 pi-Cation interactions: D:R.42

4 x MDN: METHYLENEDIPHOSPHONIC ACID(Non-covalent)

MDN.2: 7 residues within 4Å: Chain A: D.33, E.34, S.35, S.38, K.107, K.146, R.148 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.33, A:S.38, A:K.107, A:K.146, A:R.148 Water bridges: A:D.33 MDN.5: 7 residues within 4Å: Chain B: D.33, E.34, S.35, S.38, K.107, K.146, R.148 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.33, B:S.35, B:S.35, B:S.35, B:S.38, B:K.107, B:K.146, B:R.148 Water bridges: B:R.148 MDN.7: 6 residues within 4Å: Chain C: D.33, E.34, S.38, K.107, K.146, R.148 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.38, C:K.107, C:K.146, C:R.148 Water bridges: C:S.38, C:R.148 MDN.10: 6 residues within 4Å: Chain D: E.34, S.35, S.38, K.107, K.146, R.148 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.35, D:S.35, D:S.38, D:S.38, D:K.107, D:K.146, D:R.148 Water bridges: D:R.148

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 12 residues within 4Å: Chain A: L.127, E.165, N.168, V.169, R.172 Chain B: T.123, T.124, L.127, E.165, N.168, V.169, R.172 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.165, A:N.168, A:R.172, B:T.123, B:E.165, B:N.168 Water bridges: A:T.123, A:R.172 GOL.8: 11 residues within 4Å: Chain C: L.127, E.165, N.168, V.169, R.172 Chain D: T.123, L.127, E.165, N.168, V.169, R.172 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:E.165, C:E.165, C:N.168, C:R.172 Water bridges: D:T.124, C:R.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heron, P.W. et al., Bisphosphonate Inhibitors of Mammalian Glycolytic Aldolase. J.Med.Chem. (2018)

Release Date

2017-10-25

Peptides

Fructose-bisphosphate aldolase A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Fructose-bisphosphate aldolase A

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