SMTL ID : 7nls.1

Crystal structure of Mycobacterium tuberculosis ArgB in complex with methyl 4-hydroxy-3-iodobenzoate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-hexamer

Ligands

6 x 98T: methyl 3-iodanyl-4-oxidanyl-benzoate(Non-covalent)

98T.1: 8 residues within 4Å: Chain A: I.130, D.134, L.171, R.176 Chain F: V.128, I.130, L.171 Ligands: 98T.11 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:I.130, F:L.171, A:L.171 Salt bridges: A:R.176 98T.3: 8 residues within 4Å: Chain B: I.130, D.134, L.171, R.176 Chain E: V.128, I.130, L.171 Ligands: 98T.9 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:L.171, E:I.130, E:L.171 Salt bridges: B:R.176 98T.5: 8 residues within 4Å: Chain C: I.130, D.134, L.171, R.176 Chain D: V.128, I.130, L.171 Ligands: 98T.7 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.130, D:L.171, C:L.171 Salt bridges: C:R.176 98T.7: 8 residues within 4Å: Chain C: V.128, I.130, L.171 Chain D: I.130, D.134, L.171, R.176 Ligands: 98T.5 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.130, C:L.171, D:L.171 Salt bridges: D:R.176 98T.9: 8 residues within 4Å: Chain B: V.128, I.130, L.171 Chain E: I.130, D.134, L.171, R.176 Ligands: 98T.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:I.130, B:L.171, E:L.171 Salt bridges: E:R.176 98T.11: 8 residues within 4Å: Chain A: V.128, I.130, L.171 Chain F: I.130, D.134, L.171, R.176 Ligands: 98T.1 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:L.171, A:I.130, A:L.171 Salt bridges: F:R.176

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.81, F.89, R.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.94 Salt bridges: A:R.81 SO4.4: 3 residues within 4Å: Chain B: R.81, F.89, R.94 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.94 Salt bridges: B:R.81 SO4.6: 3 residues within 4Å: Chain C: R.81, F.89, R.94 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.94 Salt bridges: C:R.81 SO4.8: 3 residues within 4Å: Chain D: R.81, F.89, R.94 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.94 Salt bridges: D:R.81 SO4.10: 3 residues within 4Å: Chain E: R.81, F.89, R.94 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.94 Salt bridges: E:R.81 SO4.12: 3 residues within 4Å: Chain F: R.81, F.89, R.94 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.94 Salt bridges: F:R.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gupta, P. et al., A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis. Comput Struct Biotechnol J (2021)

Release Date

2021-06-30

Peptides

Acetylglutamate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Acetylglutamate kinase

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