SMTL ID : 4lv4.1

A noncompetitive inhibitor for M. tuberculosis's class IIa fructose 1,6-bisphosphate aldolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.96, H.252 Ligands: 8HC.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.96, A:H.252 ZN.2: 2 residues within 4Å: Chain A: H.344, H.346 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.344, A:H.346, H2O.2 ZN.7: 3 residues within 4Å: Chain B: H.96, H.252 Ligands: 8HC.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.96, B:H.252 ZN.8: 2 residues within 4Å: Chain B: H.344, H.346 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.344, B:H.346, H2O.16 ZN.13: 3 residues within 4Å: Chain C: H.96, H.252 Ligands: 8HC.15 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.96, C:H.252 ZN.14: 2 residues within 4Å: Chain C: H.344, H.346 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.344, C:H.346, H2O.29 ZN.19: 3 residues within 4Å: Chain D: H.96, H.252 Ligands: 8HC.21 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.96, D:H.252 ZN.20: 2 residues within 4Å: Chain D: H.344, H.346 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.344, D:H.346, H2O.43

4 x 8HC: 8-hydroxyquinoline-2-carboxylic acid(Non-covalent)

8HC.3: 10 residues within 4Å: Chain A: H.96, E.161, V.165, E.178, K.179, L.180, T.207, H.252, G.253 Ligands: ZN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.178, A:T.207 Hydrogen bonds: A:E.161 Water bridges: A:N.274 Salt bridges: A:H.96, A:H.252 8HC.9: 10 residues within 4Å: Chain B: H.96, E.161, V.165, E.178, K.179, L.180, T.207, H.252, G.253 Ligands: ZN.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.178, B:T.207 Hydrogen bonds: B:E.161 Water bridges: B:N.274 Salt bridges: B:H.96, B:H.252 8HC.15: 10 residues within 4Å: Chain C: H.96, E.161, V.165, E.178, K.179, L.180, T.207, H.252, G.253 Ligands: ZN.13 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:E.178, C:T.207 Hydrogen bonds: C:E.161 Water bridges: C:N.274 Salt bridges: C:H.96, C:H.252 8HC.21: 10 residues within 4Å: Chain D: H.96, E.161, V.165, E.178, K.179, L.180, T.207, H.252, G.253 Ligands: ZN.19 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:E.178, D:T.207 Hydrogen bonds: D:E.161 Water bridges: D:N.274 Salt bridges: D:H.96, D:H.252

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 7 residues within 4Å: Chain A: A.196, G.197, G.200, K.201, Y.202, P.246, D.248 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.202 Hydrogen bonds: A:Y.202, A:D.248 Salt bridges: A:K.17, A:K.201 ACT.5: 4 residues within 4Å: Chain A: L.63, G.64, V.65, K.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.64 Salt bridges: A:K.66 ACT.10: 7 residues within 4Å: Chain B: A.196, G.197, G.200, K.201, Y.202, P.246, D.248 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.202 Hydrogen bonds: B:Y.202, B:D.248 Salt bridges: B:K.17, B:K.201 ACT.11: 4 residues within 4Å: Chain B: L.63, G.64, V.65, K.66 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.64 Salt bridges: B:K.66 ACT.16: 7 residues within 4Å: Chain C: A.196, G.197, G.200, K.201, Y.202, P.246, D.248 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.202 Hydrogen bonds: C:Y.202, C:D.248 Salt bridges: C:K.17, C:K.201 ACT.17: 4 residues within 4Å: Chain C: L.63, G.64, V.65, K.66 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.64 Salt bridges: C:K.66 ACT.22: 7 residues within 4Å: Chain D: A.196, G.197, G.200, K.201, Y.202, P.246, D.248 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.202 Hydrogen bonds: D:Y.202, D:D.248 Salt bridges: D:K.17, D:K.201 ACT.23: 4 residues within 4Å: Chain D: L.63, G.64, V.65, K.66 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.64 Salt bridges: D:K.66

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 9 residues within 4Å: Chain A: K.300, E.304, V.305, Y.311 Chain B: T.277, D.278, Y.281 Chain C: D.302, G.303 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.300, A:K.300 Water bridges: B:A.282 1PE.12: 9 residues within 4Å: Chain A: T.277, D.278, Y.281 Chain B: K.300, E.304, V.305, Y.311 Chain D: D.302, G.303 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.300, B:K.300 Water bridges: A:A.282 1PE.18: 9 residues within 4Å: Chain A: D.302, G.303 Chain C: K.300, E.304, V.305, Y.311 Chain D: T.277, D.278, Y.281 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:D.302, C:K.300, C:K.300 Water bridges: D:A.282 1PE.24: 9 residues within 4Å: Chain B: D.302, G.303 Chain C: T.277, D.278, Y.281 Chain D: K.300, E.304, V.305, Y.311 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: D:K.300, D:K.300, B:D.302 Water bridges: C:A.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Capodagli, G.C. et al., A Noncompetitive Inhibitor for Mycobacterium tuberculosis's Class IIa Fructose 1,6-Bisphosphate Aldolase. Biochemistry (2014)

Release Date

2014-01-08

Peptides

Fructose-bisphosphate aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Fructose-bisphosphate aldolase

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