SMTL ID : 4ns3.1

Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis bound with NAD and cobalamin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 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 14 PLIP interactions: 13 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:I.206, A:F.266, A:F.283, A:T.289 Hydrogen bonds: A:F.266, A:A.288 Water bridges: A:T.207, A:S.269, A:S.269, A:S.286, A:T.289, A:H.292 pi-Stacking: A:F.266 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 20 PLIP interactions: 18 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Hydrophobic interactions: B:I.206, B:F.266, B:F.266, B:F.266, B:F.283, B:T.289 Hydrogen bonds: B:F.266, B:A.288, B:R.393, B:R.393 Water bridges: B:T.207, B:S.269, B:S.269, B:D.270, B:T.289, B:T.289, B:T.289 pi-Stacking: B:F.266 Metal complexes: B12.2, H2O.25 B12.3: 7 residues within 4Å: Chain C: I.206, F.266, D.270, F.283, T.289, H.292, R.393 15 PLIP interactions: 14 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:I.206, C:F.266, C:F.266, C:F.283, C:T.289 Hydrogen bonds: C:F.266, C:R.393 Water bridges: C:T.207, C:S.269, C:S.269, C:S.286, C:A.288, C:H.292, C:H.292 Metal complexes: B12.3 B12.4: 8 residues within 4Å: Chain D: I.206, F.266, D.270, F.283, A.288, T.289, H.292, R.393 12 PLIP interactions: 11 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:I.206, D:F.266, D:F.283, D:T.289 Hydrogen bonds: D:F.266, D:A.288, D:R.393 Water bridges: D:S.269, D:S.269, D:S.286 pi-Stacking: D:F.266 Metal complexes: B12.4

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.5: 19 residues within 4Å: Chain E: Y.204, I.206, T.207, P.208, F.209, N.210, K.232, P.233, S.234, D.264, G.265, S.269, F.283, T.284, G.285, S.286, T.289, H.292, C.347 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:Y.204, E:T.207, E:F.209, E:K.232, E:S.269, E:S.269, E:S.286, E:T.289, E:T.289 Water bridges: E:K.232, E:S.234 NAD.6: 20 residues within 4Å: Chain F: Y.204, I.206, T.207, P.208, F.209, N.210, K.232, P.233, S.234, D.264, G.265, F.266, S.269, F.283, T.284, G.285, S.286, T.289, H.292, C.347 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:T.207, F:F.209, F:K.232, F:S.269, F:S.286, F:S.286, F:H.292 Water bridges: F:S.234, F:I.235

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

2015-01-14

Peptides

Delta-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

Delta-1-pyrroline-5-carboxylate dehydrogenase

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