SMTL ID : 1xxx.1 (1 other biounit)

Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: A.165, H.167, I.170 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.165, A:H.167, A:I.170, H2O.1, H2O.9 MG.4: 3 residues within 4Å: Chain B: A.165, H.167, I.170 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.165, B:H.167, B:I.170, H2O.12, H2O.18 MG.7: 3 residues within 4Å: Chain C: A.165, H.167, I.170 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:A.165, C:H.167, C:I.170, H2O.25 MG.10: 3 residues within 4Å: Chain D: A.165, H.167, I.170 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:A.165, D:H.167, D:I.170, H2O.30

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

CL.2: 5 residues within 4Å: Chain A: P.158, I.161, K.177, S.182, I.186 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain B: P.158, I.161, K.177, S.182, I.186 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain C: P.158, I.161, K.177, S.182, I.186 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain D: P.158, K.177, S.182, I.186 Ligand excluded by PLIP

4 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.3: 6 residues within 4Å: Chain A: D.198, D.199, A.200, C.251, M.254, S.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.198, A:M.254 DTT.6: 6 residues within 4Å: Chain B: D.198, D.199, A.200, C.251, M.254, S.255 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.198, B:A.200 DTT.9: 6 residues within 4Å: Chain C: D.198, D.199, A.200, C.251, M.254, S.255 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.198 DTT.12: 6 residues within 4Å: Chain D: D.198, D.199, A.200, C.251, M.254, S.255 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.198 Water bridges: D:S.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kefala, G. et al., Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis. Biochem.J. (2008)

Release Date

2006-02-14

Peptides

Dihydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dihydrodipicolinate synthase

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