SMTL ID : 4b5w.1

Crystal structures of divalent metal dependent pyruvate aldolase R70A mutant, HpaI, in complex with pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-hexamer

Ligands

6 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: Q.147, E.149, G.172, D.175 Ligands: PYR.3 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:E.149, A:D.175, PYR.3, H2O.4, H2O.4 CO.4: 5 residues within 4Å: Chain B: Q.147, E.149, G.172, D.175 Ligands: PYR.5 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:E.149, B:D.175, PYR.5, H2O.18, H2O.18 CO.6: 5 residues within 4Å: Chain C: Q.147, E.149, G.172, D.175 Ligands: PYR.8 5 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: C:E.149, C:D.175, PYR.8, H2O.9, H2O.30 CO.9: 4 residues within 4Å: Chain D: Q.147, E.149, D.175 Ligands: PYR.11 5 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: D:E.149, D:D.175, PYR.11, H2O.40, H2O.40 CO.12: 5 residues within 4Å: Chain E: Q.147, E.149, G.172, D.175 Ligands: PYR.14 5 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: E:E.149, E:D.175, PYR.14, H2O.53, H2O.53 CO.15: 6 residues within 4Å: Chain F: M.94, Q.147, E.149, G.172, D.175 Ligands: PYR.17 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.149, F:D.175, H2O.45, H2O.64

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: D.133, K.137 No protein-ligand interaction detected (PLIP) CA.7: 1 residues within 4Å: Chain C: D.162 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.162, H2O.35, H2O.38 CA.10: 2 residues within 4Å: Chain A: A.252 Chain D: D.37 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.37, H2O.14, H2O.14, H2O.40, H2O.40, H2O.40 CA.13: 2 residues within 4Å: Chain E: D.162, S.205 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.162, H2O.58, H2O.62 CA.16: 1 residues within 4Å: Chain F: D.140 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.140, H2O.68

6 x PYR: PYRUVIC ACID(Non-covalent)

PYR.3: 11 residues within 4Å: Chain A: W.19, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Chain B: V.118 Ligands: CO.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.19, A:F.170, A:L.212 Hydrogen bonds: A:Q.147, A:A.174, A:D.175 Water bridges: A:E.44, A:E.44 PYR.5: 11 residues within 4Å: Chain B: W.19, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Chain C: V.118 Ligands: CO.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.19, B:F.170, B:L.212 Hydrogen bonds: B:Q.147, B:A.174, B:D.175 PYR.8: 11 residues within 4Å: Chain A: V.118 Chain C: W.19, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.6 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.19, C:F.170 Hydrogen bonds: C:Q.147, C:A.174, C:D.175 PYR.11: 11 residues within 4Å: Chain D: W.19, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Chain E: V.118 Ligands: CO.9 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.19, D:F.170, D:L.212 Hydrogen bonds: D:Q.147, D:A.174, D:D.175 PYR.14: 10 residues within 4Å: Chain E: W.19, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.12 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:W.19, E:F.170, E:L.212 Hydrogen bonds: E:Q.147, E:A.174, E:D.175 Water bridges: E:E.44, E:E.44 PYR.17: 11 residues within 4Å: Chain D: V.118 Chain F: W.19, Q.147, E.149, F.170, G.172, P.173, A.174, D.175, L.212 Ligands: CO.15 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:W.19, F:F.170, F:L.212 Hydrogen bonds: F:Q.147, F:A.174, F:D.175

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
C

D
D

E
E

F
F

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