SMTL ID : 1ojr.1

L-rhamnulose-1-phosphate aldolase from Escherichia coli (mutant E192A)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.141, H.143, H.212 Ligands: PO4.3, 2HA.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.141, A:H.143, A:H.212, H2O.20 ZN.10: 5 residues within 4Å: Chain B: H.141, H.143, H.212 Ligands: PO4.12, 2HA.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.141, B:H.143, B:H.212, H2O.40 ZN.19: 5 residues within 4Å: Chain C: H.141, H.143, H.212 Ligands: PO4.21, 2HA.22 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.141, C:H.143, C:H.212, H2O.60 ZN.28: 5 residues within 4Å: Chain D: H.141, H.143, H.212 Ligands: PO4.30, 2HA.31 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.141, D:H.143, D:H.212, H2O.80

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

PO4.2: 10 residues within 4Å: Chain A: N.29, G.31, N.32, G.74, S.75, G.76, T.115, S.116 Ligands: PO4.3, 2HA.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.29, A:N.32, A:G.76, A:S.116 Water bridges: A:S.116, A:S.116 PO4.3: 10 residues within 4Å: Chain A: G.31, N.32, E.117, H.141, H.143, H.212 Ligands: ZN.1, PO4.2, 2HA.4, GOL.6 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:G.31, A:N.32, A:E.117 Water bridges: A:N.29, A:S.116, A:S.116, A:E.117, C:E.171, C:E.171, C:E.171 Salt bridges: A:H.141, A:H.143, A:H.212 PO4.11: 10 residues within 4Å: Chain B: N.29, G.31, N.32, G.74, S.75, G.76, T.115, S.116 Ligands: PO4.12, 2HA.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.29, B:N.32, B:G.76, B:S.116 Water bridges: B:S.116, B:S.116 PO4.12: 10 residues within 4Å: Chain B: G.31, N.32, E.117, H.141, H.143, H.212 Ligands: ZN.10, PO4.11, 2HA.13, GOL.15 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Water bridges: A:E.171, A:E.171, A:E.171, B:N.29, B:S.116, B:S.116, B:E.117 Hydrogen bonds: B:G.31, B:N.32, B:E.117 Salt bridges: B:H.141, B:H.143, B:H.212 PO4.20: 10 residues within 4Å: Chain C: N.29, G.31, N.32, G.74, S.75, G.76, T.115, S.116 Ligands: PO4.21, 2HA.22 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.29, C:N.32, C:G.76, C:S.116 Water bridges: C:S.116, C:S.116 PO4.21: 10 residues within 4Å: Chain C: G.31, N.32, E.117, H.141, H.143, H.212 Ligands: ZN.19, PO4.20, 2HA.22, GOL.24 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.31, C:N.32, C:E.117 Water bridges: C:N.29, C:S.116, C:S.116, C:E.117, D:E.171, D:E.171, D:E.171 Salt bridges: C:H.141, C:H.143, C:H.212 PO4.29: 10 residues within 4Å: Chain D: N.29, G.31, N.32, G.74, S.75, G.76, T.115, S.116 Ligands: PO4.30, 2HA.31 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.29, D:N.32, D:G.76, D:S.116 Water bridges: D:S.116, D:S.116 PO4.30: 10 residues within 4Å: Chain D: G.31, N.32, E.117, H.141, H.143, H.212 Ligands: ZN.28, PO4.29, 2HA.31, GOL.33 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:G.31, D:N.32, D:E.117 Water bridges: D:N.29, D:S.116, D:S.116, D:E.117, B:E.171, B:E.171, B:E.171 Salt bridges: D:H.141, D:H.143, D:H.212

4 x 2HA: Dihydroxyacetone(Non-covalent)

2HA.4: 13 residues within 4Å: Chain A: N.29, G.30, G.31, N.32, E.117, H.141, H.143, W.209, H.212 Ligands: ZN.1, PO4.2, PO4.3, GOL.6 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain A Water bridges: C:E.171, C:E.171, A:R.28, A:N.29, A:N.29 Hydrogen bonds: A:G.31, A:N.32, A:E.117 2HA.13: 13 residues within 4Å: Chain B: N.29, G.30, G.31, N.32, E.117, H.141, H.143, W.209, H.212 Ligands: ZN.10, PO4.11, PO4.12, GOL.15 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.31, B:N.32, B:E.117 Water bridges: B:R.28, B:N.29, B:N.29, A:E.171, A:E.171 2HA.22: 13 residues within 4Å: Chain C: N.29, G.30, G.31, N.32, E.117, H.141, H.143, W.209, H.212 Ligands: ZN.19, PO4.20, PO4.21, GOL.24 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain C Water bridges: D:E.171, D:E.171, C:R.28, C:N.29, C:N.29 Hydrogen bonds: C:G.31, C:N.32, C:E.117 2HA.31: 13 residues within 4Å: Chain D: N.29, G.30, G.31, N.32, E.117, H.141, H.143, W.209, H.212 Ligands: ZN.28, PO4.29, PO4.30, GOL.33 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain D Water bridges: B:E.171, B:E.171, D:R.28, D:N.29, D:N.29 Hydrogen bonds: D:G.31, D:N.32, D:E.117

4 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.5: 4 residues within 4Å: Chain A: H.46, D.47, F.49, Q.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.51 DIO.14: 4 residues within 4Å: Chain B: H.46, D.47, F.49, Q.51 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.51 DIO.23: 4 residues within 4Å: Chain C: H.46, D.47, F.49, Q.51 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.51 DIO.32: 4 residues within 4Å: Chain D: H.46, D.47, F.49, Q.51 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.51

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: R.28, N.29, P.188 Chain C: E.171, F.263 Ligands: PO4.3, 2HA.4 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: G.76, K.77, F.78, N.81 Chain C: D.222, E.223 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: R.80, Q.83, L.84 Chain C: L.22 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: V.153, L.154, Y.242 Chain C: M.244, K.248 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain A: E.171, F.263 Chain B: R.28, N.29, P.188 Ligands: PO4.12, 2HA.13 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain A: D.222, E.223 Chain B: G.76, K.77, F.78, N.81 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain A: L.22 Chain B: R.80, Q.83, L.84 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain A: M.244, K.248 Chain B: V.153, L.154, Y.242 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain C: R.28, N.29, P.188 Chain D: E.171, F.263 Ligands: PO4.21, 2HA.22 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain C: G.76, K.77, F.78, N.81 Chain D: D.222, E.223 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain C: R.80, Q.83, L.84 Chain D: L.22 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain C: V.153, L.154, Y.242 Chain D: M.244, K.248 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain B: E.171, F.263 Chain D: R.28, N.29, P.188 Ligands: PO4.30, 2HA.31 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain B: D.222, E.223 Chain D: G.76, K.77, F.78, N.81 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain B: L.22 Chain D: R.80, Q.83, L.84 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain B: M.244, K.248 Chain D: V.153, L.154, Y.242 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kroemer, M. et al., Structure and Catalytic Mechanism of L-Rhamnulose-1-Phosphate Aldolase. Biochemistry (2003)

Release Date

2003-09-11

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