SMTL ID : 6p1y.1

Crystal structure of Mtb aspartate decarboxylase mutant M117I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

hetero-4-4-mer

Ligands

4 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.1: 4 residues within 4Å: Chain A: V.23 Chain E: K.9, R.12 Ligands: TLA.2 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.9, E:K.9, E:R.12 NH4.3: 4 residues within 4Å: Chain C: V.23 Chain G: K.9, R.12 Ligands: TLA.4 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain G Hydrogen bonds: C:Y.22, G:K.9, G:R.12 NH4.5: 4 residues within 4Å: Chain C: K.9, R.12 Chain E: V.23 Ligands: TLA.6 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:K.9, C:R.12, E:Y.22 NH4.7: 4 residues within 4Å: Chain A: K.9, R.12 Chain G: V.23 Ligands: TLA.8 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain G Hydrogen bonds: A:K.9, A:R.12, G:V.23

4 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.2: 13 residues within 4Å: Chain B: X.1, T.33, Y.34, N.48, G.49, A.50, A.51 Chain E: K.9 Chain F: V.23, I.25, R.30, I.62 Ligands: NH4.1 8 PLIP interactions: 4 interactions with chain B, 1 interactions with chain F, 3 interactions with chain E Hydrogen bonds: B:T.33, B:N.48, B:A.50, B:A.51 Salt bridges: F:R.30, E:K.9 Water bridges: E:R.12, E:R.12 TLA.4: 13 residues within 4Å: Chain D: X.1, T.33, Y.34, N.48, G.49, A.50, A.51 Chain G: K.9 Chain H: V.23, I.25, R.30, I.62 Ligands: NH4.3 8 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H, 4 interactions with chain D Water bridges: G:R.12, G:R.12 Salt bridges: G:K.9, H:R.30 Hydrogen bonds: D:T.33, D:N.48, D:A.50, D:A.51 TLA.6: 13 residues within 4Å: Chain C: K.9 Chain D: V.23, I.25, R.30, I.62 Chain F: X.1, T.33, Y.34, N.48, G.49, A.50, A.51 Ligands: NH4.5 8 PLIP interactions: 4 interactions with chain F, 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: F:T.33, F:N.48, F:A.50, F:A.51 Water bridges: C:R.12, C:R.12 Salt bridges: C:K.9, D:R.30 TLA.8: 13 residues within 4Å: Chain A: K.9 Chain B: V.23, I.25, R.30, I.62 Chain H: X.1, T.33, Y.34, N.48, G.49, A.50, A.51 Ligands: NH4.7 8 PLIP interactions: 4 interactions with chain H, 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: H:T.33, H:N.48, H:A.50, H:A.51 Salt bridges: B:R.30, A:K.9 Water bridges: A:R.12, A:R.12

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
A

E
A

G
A

B
B

D
B

F
B

H
B

Aspartate 1-decarboxylase beta chain

Aspartate 1-decarboxylase alpha chain

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