SMTL ID : 2v2b.1

L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E117S- E192A-K248G-R253A-E254A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.141, H.143, H.212 Ligands: ACT.3 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.141, A:H.143, A:H.212, ACT.3, H2O.9 ZN.2: 2 residues within 4Å: Chain A: E.200, H.204 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.200, A:E.200, A:H.204 ZN.6: 4 residues within 4Å: Chain B: H.141, H.143, H.212 Ligands: ACT.8 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:H.141, B:H.143, B:H.212, ACT.8, H2O.17 ZN.7: 2 residues within 4Å: Chain B: E.200, H.204 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.200, B:E.200, B:H.204 ZN.11: 4 residues within 4Å: Chain C: H.141, H.143, H.212 Ligands: ACT.13 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:H.141, C:H.143, C:H.212, ACT.13, H2O.25 ZN.12: 2 residues within 4Å: Chain C: E.200, H.204 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.200, C:E.200, C:H.204 ZN.16: 4 residues within 4Å: Chain D: H.141, H.143, H.212 Ligands: ACT.18 5 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: D:H.141, D:H.143, D:H.212, ACT.18, H2O.34 ZN.17: 2 residues within 4Å: Chain D: E.200, H.204 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.200, D:E.200, D:H.204

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

ACT.3: 9 residues within 4Å: Chain A: N.29, G.30, G.31, N.32, H.141, H.143, H.212 Ligands: ZN.1, PO4.5 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.31, A:N.32 Salt bridges: A:H.141, A:H.143, A:H.212 Water bridges: B:E.171 ACT.8: 9 residues within 4Å: Chain B: N.29, G.30, G.31, N.32, H.141, H.143, H.212 Ligands: ZN.6, PO4.10 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.31, B:N.32 Salt bridges: B:H.141, B:H.143, B:H.212 Water bridges: D:E.171 ACT.13: 9 residues within 4Å: Chain C: N.29, G.30, G.31, N.32, H.141, H.143, H.212 Ligands: ZN.11, PO4.15 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.31, C:N.32 Salt bridges: C:H.141, C:H.143, C:H.212 Water bridges: A:E.171 ACT.18: 9 residues within 4Å: Chain D: N.29, G.30, G.31, N.32, H.141, H.143, H.212 Ligands: ZN.16, PO4.20 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.31, D:N.32 Salt bridges: D:H.141, D:H.143, D:H.212 Water bridges: C:E.171

4 x PGR: R-1,2-PROPANEDIOL(Non-covalent)

PGR.4: 3 residues within 4Å: Chain A: R.80, Q.83, L.84 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:D.19 Hydrogen bonds: A:R.80, A:R.80, A:Q.83 PGR.9: 3 residues within 4Å: Chain B: R.80, Q.83, L.84 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.80, B:R.80, B:Q.83 Water bridges: D:D.19 PGR.14: 3 residues within 4Å: Chain C: R.80, Q.83, L.84 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Water bridges: A:D.19 Hydrogen bonds: C:R.80, C:R.80, C:Q.83 PGR.19: 3 residues within 4Å: Chain D: R.80, Q.83, L.84 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.80, D:R.80, D:Q.83 Water bridges: C:D.19

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

PO4.5: 7 residues within 4Å: Chain A: N.29, N.32, S.75, G.76, T.115, S.116 Ligands: ACT.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.29, A:N.32, A:G.76, A:S.116 Water bridges: A:N.29, A:S.117, A:S.117 PO4.10: 7 residues within 4Å: Chain B: N.29, N.32, S.75, G.76, T.115, S.116 Ligands: ACT.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.29, B:N.32, B:G.76, B:S.116 Water bridges: B:N.29, B:S.117, B:S.117 PO4.15: 7 residues within 4Å: Chain C: N.29, N.32, S.75, G.76, T.115, S.116 Ligands: ACT.13 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.29, C:N.32, C:G.76, C:S.116 Water bridges: C:N.29, C:S.117, C:S.117 PO4.20: 7 residues within 4Å: Chain D: N.29, N.32, S.75, G.76, T.115, S.116 Ligands: ACT.18 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.29, D:N.32, D:G.76, D:S.116 Water bridges: D:N.29, D:S.117, D:S.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grueninger, D. et al., Antenna Domain Mobility and Enzymatic Reaction of L-Rhamnulose-1-Phosphate Aldolase. Biochemistry (2008)

Release Date

2008-01-08

Peptides

RHAMNULOSE-1-PHOSPHATE ALDOLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

RHAMNULOSE-1-PHOSPHATE ALDOLASE