SMTL ID : 7nlw.1

Crystal structure of Mycobacterium tuberculosis ArgB in complex with 2-(5-methoxy-1H-indol-3-yl)acetonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-hexamer

Ligands

6 x UOK: 2-(5-methoxy-1~{H}-indol-3-yl)ethanenitrile(Non-covalent)

UOK.1: 10 residues within 4Å: Chain A: V.128, I.130, L.171, R.176 Chain F: V.128, I.130, A.135, L.171, R.176 Ligands: UOK.16 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:V.128, F:L.171, F:L.171, A:I.130, A:L.171 Hydrogen bonds: A:R.176 UOK.4: 10 residues within 4Å: Chain B: V.128, I.130, L.171, R.176 Chain E: V.128, I.130, A.135, L.171, R.176 Ligands: UOK.13 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain B Hydrophobic interactions: E:V.128, E:L.171, E:L.171, B:I.130, B:L.171 Hydrogen bonds: B:R.176 UOK.7: 10 residues within 4Å: Chain C: V.128, I.130, L.171, R.176 Chain D: V.128, I.130, A.135, L.171, R.176 Ligands: UOK.10 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.130, C:L.171, D:V.128, D:L.171, D:L.171 Hydrogen bonds: C:R.176 UOK.10: 10 residues within 4Å: Chain C: V.128, I.130, A.135, L.171, R.176 Chain D: V.128, I.130, L.171, R.176 Ligands: UOK.7 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.128, C:L.171, C:L.171, D:I.130, D:L.171 Hydrogen bonds: D:R.176 UOK.13: 10 residues within 4Å: Chain B: V.128, I.130, A.135, L.171, R.176 Chain E: V.128, I.130, L.171, R.176 Ligands: UOK.4 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain B Hydrophobic interactions: E:I.130, E:L.171, B:V.128, B:L.171, B:L.171 Hydrogen bonds: E:R.176 UOK.16: 10 residues within 4Å: Chain A: V.128, I.130, A.135, L.171, R.176 Chain F: V.128, I.130, L.171, R.176 Ligands: UOK.1 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:I.130, F:L.171, A:V.128, A:L.171, A:L.171 Hydrogen bonds: F:R.176

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

SO4.2: 5 residues within 4Å: Chain A: W.25, Q.28, K.211, H.270, K.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.28 Salt bridges: A:K.211, A:H.270 SO4.3: 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 SO4.5: 5 residues within 4Å: Chain B: W.25, Q.28, K.211, H.270, K.293 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.28 Salt bridges: B:K.211, B:H.270 SO4.6: 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 SO4.8: 5 residues within 4Å: Chain C: W.25, Q.28, K.211, H.270, K.293 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.28 Salt bridges: C:K.211, C:H.270 SO4.9: 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 SO4.11: 5 residues within 4Å: Chain D: W.25, Q.28, K.211, H.270, K.293 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.28 Salt bridges: D:K.211, D:H.270 SO4.12: 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 SO4.14: 5 residues within 4Å: Chain E: W.25, Q.28, K.211, H.270, K.293 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.28 Salt bridges: E:K.211, E:H.270 SO4.15: 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 SO4.17: 5 residues within 4Å: Chain F: W.25, Q.28, K.211, H.270, K.293 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.28 Salt bridges: F:K.211, F:H.270 SO4.18: 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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