SMTL ID : 4del.1

Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: V.211, G.213, G.253, S.255 Ligands: PGH.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.211, A:G.213 Water bridges: A:V.211 NA.7: 5 residues within 4Å: Chain B: V.211, G.213, G.253, S.255 Ligands: PGH.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.213, B:S.255 Water bridges: B:V.211 NA.13: 5 residues within 4Å: Chain C: V.211, G.213, G.253, S.255 Ligands: PGH.16 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.213, C:S.255 Water bridges: C:V.211 NA.19: 5 residues within 4Å: Chain D: V.211, G.213, G.253, S.255 Ligands: PGH.22 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.211, D:G.213 Water bridges: D:V.211

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.96, H.212, H.252 Ligands: PGH.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.96, A:H.212, A:H.252 ZN.3: 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.19 ZN.8: 4 residues within 4Å: Chain B: H.96, H.212, H.252 Ligands: PGH.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.96, B:H.212, B:H.252 ZN.9: 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.39 ZN.14: 4 residues within 4Å: Chain C: H.96, H.212, H.252 Ligands: PGH.16 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.96, C:H.212, C:H.252 ZN.15: 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.59 ZN.20: 4 residues within 4Å: Chain D: H.96, H.212, H.252 Ligands: PGH.22 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.96, D:H.212, D:H.252 ZN.21: 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.79

4 x PGH: PHOSPHOGLYCOLOHYDROXAMIC ACID(Non-covalent)

PGH.4: 17 residues within 4Å: Chain A: N.27, Q.51, D.95, H.96, V.211, H.212, G.213, H.252, G.253, G.254, S.255, N.274, V.275, D.276, T.277 Ligands: NA.1, ZN.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.27, A:Q.51, A:G.213, A:G.253, A:G.254, A:S.255, A:S.255, A:N.274, A:D.276, A:T.277 Water bridges: A:T.277, B:K.308 PGH.10: 17 residues within 4Å: Chain B: N.27, Q.51, D.95, H.96, V.211, H.212, G.213, H.252, G.253, G.254, S.255, N.274, V.275, D.276, T.277 Ligands: NA.7, ZN.8 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.27, B:Q.51, B:G.213, B:G.253, B:G.254, B:S.255, B:S.255, B:N.274, B:D.276, B:T.277 Water bridges: B:T.277, A:K.308 PGH.16: 17 residues within 4Å: Chain C: N.27, Q.51, D.95, H.96, V.211, H.212, G.213, H.252, G.253, G.254, S.255, N.274, V.275, D.276, T.277 Ligands: NA.13, ZN.14 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.27, C:Q.51, C:H.212, C:G.213, C:H.252, C:G.253, C:G.254, C:S.255, C:S.255, C:N.274, C:D.276, C:T.277, C:T.277 Water bridges: C:D.95, C:D.95, C:T.277, D:K.308 PGH.22: 17 residues within 4Å: Chain D: N.27, Q.51, D.95, H.96, V.211, H.212, G.213, H.252, G.253, G.254, S.255, N.274, V.275, D.276, T.277 Ligands: NA.19, ZN.20 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.27, D:Q.51, D:G.213, D:G.253, D:G.254, D:S.255, D:S.255, D:N.274, D:D.276, D:T.277, D:T.277 Water bridges: D:D.95, D:D.95, D:T.277, C:K.308

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

ACT.5: 6 residues within 4Å: Chain A: L.13, G.14, K.17, K.201, D.248 Ligands: P6G.6 6 PLIP interactions: 6 interactions with chain A Water bridges: A:A.10, A:G.14, A:K.17, A:D.248 Salt bridges: A:K.17, A:K.201 ACT.11: 6 residues within 4Å: Chain B: L.13, G.14, K.17, K.201, D.248 Ligands: P6G.12 6 PLIP interactions: 6 interactions with chain B Water bridges: B:A.10, B:G.14, B:K.17, B:D.248 Salt bridges: B:K.17, B:K.201 ACT.17: 6 residues within 4Å: Chain C: L.13, G.14, K.17, K.201, D.248 Ligands: P6G.18 5 PLIP interactions: 5 interactions with chain C Water bridges: C:A.10, C:G.14, C:K.17 Salt bridges: C:K.17, C:K.201 ACT.23: 6 residues within 4Å: Chain D: L.13, G.14, K.17, K.201, D.248 Ligands: P6G.24 5 PLIP interactions: 5 interactions with chain D Water bridges: D:A.10, D:G.14, D:K.17 Salt bridges: D:K.17, D:K.201

4 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.6: 11 residues within 4Å: Chain A: A.10, E.11, G.14, A.196, G.197, G.200, K.201, Y.202, P.246, D.248 Ligands: ACT.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.200, A:K.201, A:Y.202 Water bridges: A:E.11, A:E.11, A:G.14, A:D.248 P6G.12: 11 residues within 4Å: Chain B: A.10, E.11, G.14, A.196, G.197, G.200, K.201, Y.202, P.246, D.248 Ligands: ACT.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.200, B:K.201, B:Y.202 Water bridges: B:E.11, B:E.11, B:G.14, B:D.248 P6G.18: 11 residues within 4Å: Chain C: A.10, E.11, G.14, A.196, G.197, G.200, K.201, Y.202, P.246, D.248 Ligands: ACT.17 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.200, C:K.201, C:Y.202 Water bridges: C:E.11, C:E.11, C:G.14 P6G.24: 11 residues within 4Å: Chain D: A.10, E.11, G.14, A.196, G.197, G.200, K.201, Y.202, P.246, D.248 Ligands: ACT.23 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.200, D:K.201, D:Y.202 Water bridges: D:E.11, D:E.11, D:G.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pegan, S.D. et al., Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis. Biochemistry (2013)

Release Date

2013-01-23

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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