SMTL ID : 7nlu.1

Crystal structure of Mycobacterium tuberculosis ArgB in complex with 1-(1H-indol-3-yl)ethan-1-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: W.25, Q.28, K.211, K.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.28 Salt bridges: A:K.211, A:H.270 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: 4 residues within 4Å: Chain B: W.25, Q.28, K.211, K.293 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.28 Salt bridges: B:K.211, B:H.270 SO4.5: 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 SO4.7: 4 residues within 4Å: Chain C: W.25, Q.28, K.211, K.293 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.28 Salt bridges: C:K.211, C:H.270 SO4.8: 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 SO4.10: 4 residues within 4Å: Chain D: W.25, Q.28, K.211, K.293 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.28 Salt bridges: D:K.211, D:H.270 SO4.11: 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 SO4.13: 4 residues within 4Å: Chain E: W.25, Q.28, K.211, K.293 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.28 Salt bridges: E:K.211, E:H.270 SO4.14: 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 SO4.16: 4 residues within 4Å: Chain F: W.25, Q.28, K.211, K.293 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.28 Salt bridges: F:K.211, F:H.270 SO4.17: 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

6 x 5RN: 1-(1~{H}-indol-3-yl)ethanone(Non-covalent)

5RN.3: 8 residues within 4Å: Chain A: V.128, I.130, L.171 Chain F: V.128, I.130, L.137, L.171 Ligands: 5RN.18 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:V.128, F:L.137, F:L.171, A:V.128, A:V.128, A:L.171 5RN.6: 8 residues within 4Å: Chain B: V.128, I.130, L.171 Chain E: V.128, I.130, L.137, L.171 Ligands: 5RN.15 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:V.128, B:V.128, B:L.171, E:V.128, E:L.137, E:L.171 5RN.9: 8 residues within 4Å: Chain C: V.128, I.130, L.171 Chain D: V.128, I.130, L.137, L.171 Ligands: 5RN.12 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.128, C:V.128, C:L.171, D:V.128, D:L.137, D:L.171 5RN.12: 8 residues within 4Å: Chain C: V.128, I.130, L.137, L.171 Chain D: V.128, I.130, L.171 Ligands: 5RN.9 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.128, C:L.137, C:L.171, D:V.128, D:V.128, D:L.171 5RN.15: 8 residues within 4Å: Chain B: V.128, I.130, L.137, L.171 Chain E: V.128, I.130, L.171 Ligands: 5RN.6 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:V.128, B:L.137, B:L.171, E:V.128, E:V.128, E:L.171 5RN.18: 8 residues within 4Å: Chain A: V.128, I.130, L.137, L.171 Chain F: V.128, I.130, L.171 Ligands: 5RN.3 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:V.128, F:V.128, F:L.171, A:V.128, A:L.137, A:L.171

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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