SMTL ID : 6p02.1 (2 other biounits)

Crystal structure of Mtb aspartate decarboxylase, 6-Chlorine pyrazinoic acid complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-4-4-mer

Ligands

4 x NMJ: 6-chloropyrazine-2-carboxylic acid(Non-covalent)

NMJ.1: 13 residues within 4Å: Chain B: X.1, T.33, Y.34, N.48, G.49, A.50, A.51 Chain G: K.9 Chain H: V.23, R.30, I.62, I.64, Y.66 8 PLIP interactions: 3 interactions with chain B, 1 interactions with chain G, 4 interactions with chain H Hydrogen bonds: B:T.33, B:A.50, B:A.51, G:K.9, H:R.30, H:R.30 Salt bridges: H:R.30 Halogen bonds: H:Y.66 NMJ.2: 14 residues within 4Å: Chain A: K.9 Chain B: V.23, R.30, I.62, I.64, Y.66 Chain D: X.1, V.32, T.33, Y.34, N.48, G.49, A.50, A.51 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:T.33, D:A.50, D:A.51, B:R.30, B:R.30 Salt bridges: B:R.30 NMJ.3: 13 residues within 4Å: Chain D: V.23, R.30, I.62, I.64, Y.66 Chain F: X.1, V.32, T.33, Y.34, N.48, G.49, A.50, A.51 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain D Hydrogen bonds: F:A.50, F:A.51, D:R.30, D:R.30 Salt bridges: D:R.30 Halogen bonds: D:Y.66 NMJ.4: 13 residues within 4Å: Chain F: V.23, R.30, I.62, I.64, Y.66 Chain H: X.1, V.32, T.33, Y.34, N.48, G.49, A.50, A.51 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain H Hydrogen bonds: F:R.30, H:A.50, H:A.51 Salt bridges: F:R.30 Halogen bonds: F:Y.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Q. et al., The molecular basis of pyrazinamide activity on Mycobacterium tuberculosis PanD. Nat Commun (2020)

Release Date

2020-02-05

Peptides

Aspartate 1-decarboxylase beta chain: ACEG
Aspartate 1-decarboxylase alpha chain: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

Aspartate 1-decarboxylase beta chain

Aspartate 1-decarboxylase alpha chain

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