SMTL ID : 6oyy.2 (1 other biounit)

Crystal structure of Mtb aspartate decarboxylase, pyrazinoic acid complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-4-4-mer

Ligands

4 x VGL: PYRAZINE-2-CARBOXYLIC ACID(Non-covalent)

VGL.1: 14 residues within 4Å: Chain B: X.1, V.32, 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 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain H Hydrogen bonds: B:T.33, B:A.50, B:A.51, H:R.30 Salt bridges: H:R.30 VGL.2: 12 residues within 4Å: Chain A: K.9 Chain B: V.23, R.30, I.62, I.64 Chain D: X.1, T.33, Y.34, N.48, G.49, A.50, A.51 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:R.30, B:R.30, D:T.33, D:A.50, D:A.51 Salt bridges: B:R.30 VGL.3: 12 residues within 4Å: Chain C: K.9 Chain D: V.23, R.30, I.62, I.64 Chain F: X.1, T.33, Y.34, N.48, G.49, A.50, A.51 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:A.50, F:A.51, D:R.30 Salt bridges: D:R.30 VGL.4: 12 residues within 4Å: Chain E: K.9 Chain F: V.23, R.30, I.62, I.64 Chain H: X.1, T.33, Y.34, N.48, G.49, A.50, A.51 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain F Hydrogen bonds: H:A.50, H:A.51, F:R.30 Salt bridges: F:R.30

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
E

C
G

E
I

G
K

B
F

D
H

F
J

H
L

Aspartate 1-decarboxylase beta chain

Aspartate 1-decarboxylase alpha chain

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