SMTL ID : 4lem.4 (3 other biounits)

Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-hexamer

Ligands

4 x B12: COBALAMIN(Non-covalent)

B12.1: 8 residues within 4Å: Chain A: I.206, F.266, D.270, F.283, A.288, T.289, H.292, R.393 15 PLIP interactions: 14 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:I.206, A:F.266, A:F.266, A:F.266, A:F.283, A:T.289 Hydrogen bonds: A:F.266, A:A.288 Water bridges: A:S.269, A:S.269, A:T.289, A:T.289, A:R.393, A:R.393 Metal complexes: B12.1 B12.2: 8 residues within 4Å: Chain B: I.206, F.266, D.270, F.283, A.288, T.289, H.292, R.393 16 PLIP interactions: 15 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:I.206, B:F.266, B:F.266, B:F.283, B:T.289 Hydrogen bonds: B:F.266, B:A.288 Water bridges: B:S.269, B:S.269, B:T.289, B:T.289, B:T.289, B:R.393, B:R.393 pi-Stacking: B:F.266 Metal complexes: B12.2 B12.3: 7 residues within 4Å: Chain C: I.206, F.266, D.270, F.283, A.288, T.289, H.292 14 PLIP interactions: 13 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:I.206, C:F.266, C:F.266, C:F.283 Hydrogen bonds: C:F.266, C:D.270, C:A.288, C:T.289, C:T.289 Water bridges: C:T.207, C:S.269, C:S.269 pi-Stacking: C:F.266 Metal complexes: B12.3 B12.5: 7 residues within 4Å: Chain D: I.206, F.266, D.270, F.283, A.288, T.289, H.292 16 PLIP interactions: 15 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:I.206, D:F.266, D:F.266, D:F.266, D:F.283, D:T.289 Hydrogen bonds: D:F.266, D:A.288 Water bridges: D:S.269, D:S.269, D:S.286, D:T.289, D:R.393 pi-Stacking: D:F.266 pi-Cation interactions: D:F.266 Metal complexes: B12.5

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain C: A.405, K.406, A.408, V.411 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:A.405, C:K.406, C:A.408, C:V.411 MG.6: 4 residues within 4Å: Chain D: A.405, K.406, A.408, V.411 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:A.405, D:K.406, D:A.408, D:V.411, H2O.61 MG.7: 4 residues within 4Å: Chain F: A.405, K.406, A.408, V.411 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:A.405, F:K.406, F:A.408, F:V.411, H2O.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lagautriere, T. et al., Use of a "silver bullet" to resolve crystal lattice dislocation disorder: A cobalamin complex of Delta (1)-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis. J.Struct.Biol. (2015)

Release Date

2014-05-14

Peptides

1-pyrroline-5-carboxylate dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

1-pyrroline-5-carboxylate dehydrogenase

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