SMTL ID : 1yxd.1

Structure of E. coli dihydrodipicolinate synthase bound with allosteric inhibitor (S)-lysine to 2.0 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: A.152, V.154, K.155, I.157 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.152, A:V.154, A:I.157 K.3: 4 residues within 4Å: Chain B: A.152, V.154, K.155, I.157 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.152, B:V.154, B:I.157, H2O.18 K.8: 4 residues within 4Å: Chain C: A.152, V.154, K.155, I.157 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:A.152, C:V.154, C:I.157 K.10: 4 residues within 4Å: Chain D: A.152, V.154, K.155, I.157 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:A.152, D:V.154, D:I.157, H2O.40

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: V.40, G.43, T.44, L.101, K.161 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain B: A.8, V.40, G.43, T.44, L.101, K.161 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain C: V.40, G.43, T.44, L.101, K.161 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain D: A.8, V.40, G.43, T.44, L.101, K.161 Ligand excluded by PLIP

6 x LYS: LYSINE(Non-covalent)

LYS.5: 9 residues within 4Å: Chain A: S.48, A.49, L.51, H.53, H.56, Y.106 Chain B: N.80, E.84 Ligands: LYS.6 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.48, A:H.56, A:Y.106, B:N.80, B:N.80 Water bridges: A:N.80, A:E.84, B:N.80 LYS.6: 9 residues within 4Å: Chain A: N.80, E.84 Chain B: S.48, A.49, L.51, H.53, H.56, Y.106 Ligands: LYS.5 9 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:A.49, B:H.56, A:N.80, A:E.84, K.6 Water bridges: B:N.80, B:Y.106, A:E.84, A:Y.106 LYS.7: 1 residues within 4Å: Chain B: A.83 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Ligand interactions Water bridges: B:A.83 Hydrogen bonds: K.7, K.7 LYS.12: 9 residues within 4Å: Chain C: S.48, A.49, L.51, H.53, H.56, Y.106 Chain D: N.80, E.84 Ligands: LYS.13 8 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain C, 4 interactions with chain D Water bridges: K.13, C:E.84, C:Y.106, D:E.84, D:Y.106 Hydrogen bonds: C:H.56, D:N.80, D:N.80 LYS.13: 9 residues within 4Å: Chain C: N.80, E.84 Chain D: S.48, A.49, L.51, H.53, H.56, Y.106 Ligands: LYS.12 9 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain D, 3 interactions with chain C Hydrogen bonds: K.13, D:S.48, D:A.49, D:H.56, D:Y.106, C:N.80, C:E.84 Water bridges: D:N.80, C:N.80 LYS.14: 1 residues within 4Å: Chain D: A.83 3 PLIP interactions: 2 Ligand-Ligand interactions, 1 interactions with chain D Hydrogen bonds: K.14, K.14 Water bridges: D:A.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dobson, R.C. et al., The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance. Acta Crystallogr.,Sect.D (2005)

Release Date

2005-08-02

Peptides

dihydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

dihydrodipicolinate synthase

Related Entries With Identical Sequence