SMTL ID : 4b5x.1

Crystal structures of divalent metal dependent pyruvate aldolase (HpaI), mutant D42A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: E.44, H.45 Chain C: D.84, V.85, A.123, R.124, W.128 Chain D: Y.26 Ligand excluded by PLIP PO4.2: 7 residues within 4Å: Chain A: L.22, S.23, S.24, H.45, P.47 Chain D: S.24, Y.26 Ligand excluded by PLIP PO4.3: 5 residues within 4Å: Chain A: K.6, R.109, E.164, G.165, D.167 Ligand excluded by PLIP PO4.4: 8 residues within 4Å: Chain A: R.70, P.93, M.94, E.149, D.175 Chain C: K.80, G.117, G.119 Ligand excluded by PLIP PO4.6: 8 residues within 4Å: Chain B: E.44, H.45 Chain E: Y.26 Chain F: D.84, V.85, A.123, R.124, W.128 Ligand excluded by PLIP PO4.7: 8 residues within 4Å: Chain B: L.22, S.23, S.24, H.45, P.47 Chain E: S.24, Y.26 Chain F: Q.51 Ligand excluded by PLIP PO4.8: 6 residues within 4Å: Chain B: K.6, K.10, R.109, E.164, G.165, D.167 Ligand excluded by PLIP PO4.9: 9 residues within 4Å: Chain B: R.70, P.93, M.94, Q.147, E.149, D.175 Chain F: K.80, G.117, G.119 Ligand excluded by PLIP PO4.11: 8 residues within 4Å: Chain C: E.44, H.45 Chain E: D.84, V.85, A.123, R.124, W.128 Chain F: Y.26 Ligand excluded by PLIP PO4.12: 7 residues within 4Å: Chain C: L.22, S.23, S.24, H.45, P.47 Chain F: S.24, Y.26 Ligand excluded by PLIP PO4.13: 5 residues within 4Å: Chain C: K.6, R.109, E.164, G.165, D.167 Ligand excluded by PLIP PO4.14: 8 residues within 4Å: Chain C: R.70, P.93, M.94, E.149, D.175 Chain E: K.80, G.117, G.119 Ligand excluded by PLIP PO4.16: 8 residues within 4Å: Chain A: Y.26 Chain B: D.84, V.85, A.123, R.124, W.128 Chain D: E.44, H.45 Ligand excluded by PLIP PO4.17: 8 residues within 4Å: Chain A: S.24, Y.26 Chain B: Q.51 Chain D: L.22, S.23, S.24, H.45, P.47 Ligand excluded by PLIP PO4.18: 6 residues within 4Å: Chain D: K.6, K.10, R.109, E.164, G.165, D.167 Ligand excluded by PLIP PO4.19: 9 residues within 4Å: Chain B: K.80, G.117, G.119 Chain D: R.70, P.93, M.94, Q.147, E.149, D.175 Ligand excluded by PLIP PO4.21: 8 residues within 4Å: Chain A: D.84, V.85, A.123, R.124, W.128 Chain B: Y.26 Chain E: E.44, H.45 Ligand excluded by PLIP PO4.22: 7 residues within 4Å: Chain B: S.24, Y.26 Chain E: L.22, S.23, S.24, H.45, P.47 Ligand excluded by PLIP PO4.23: 5 residues within 4Å: Chain E: K.6, R.109, E.164, G.165, D.167 Ligand excluded by PLIP PO4.24: 8 residues within 4Å: Chain A: K.80, G.117, G.119 Chain E: R.70, P.93, M.94, E.149, D.175 Ligand excluded by PLIP PO4.26: 8 residues within 4Å: Chain C: Y.26 Chain D: D.84, V.85, A.123, R.124, W.128 Chain F: E.44, H.45 Ligand excluded by PLIP PO4.27: 8 residues within 4Å: Chain C: S.24, Y.26 Chain D: Q.51 Chain F: L.22, S.23, S.24, H.45, P.47 Ligand excluded by PLIP PO4.28: 6 residues within 4Å: Chain F: K.6, K.10, R.109, E.164, G.165, D.167 Ligand excluded by PLIP PO4.29: 9 residues within 4Å: Chain D: K.80, G.117, G.119 Chain F: R.70, P.93, M.94, Q.147, E.149, D.175 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: E.29, P.62, Y.63 Chain B: A.61, R.124, R.127 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.127, B:R.127, A:P.62 Water bridges: B:R.124 GOL.10: 6 residues within 4Å: Chain A: A.61, R.124, R.127 Chain B: E.29, P.62, Y.63 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:P.62, A:R.127, A:R.127 Water bridges: B:E.29, A:R.124 GOL.15: 6 residues within 4Å: Chain C: E.29, P.62, Y.63 Chain D: A.61, R.124, R.127 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.127, D:R.127, C:P.62 Water bridges: D:R.124 GOL.20: 6 residues within 4Å: Chain C: A.61, R.124, R.127 Chain D: E.29, P.62, Y.63 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.127, C:R.127, D:P.62 Water bridges: C:R.124, D:E.29 GOL.25: 6 residues within 4Å: Chain E: E.29, P.62, Y.63 Chain F: A.61, R.124, R.127 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:P.62, F:R.127, F:R.127 Water bridges: F:R.124 GOL.30: 6 residues within 4Å: Chain E: A.61, R.124, R.127 Chain F: E.29, P.62, Y.63 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:P.62, E:R.127, E:R.127 Water bridges: F:E.29, E:R.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coincon, M. et al., Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase: Substrate Cleavage, Enolate Stabilization and Substrate Specificity. J.Biol.Chem. (2012)

Release Date

2012-08-29

Peptides

4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE