SMTL ID : 3fhz.1

Crystal structure of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator and co-repressor, L-arginine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.27 Å

Oligo State

homo-hexamer

Ligands

9 x ARG: ARGININE(Non-covalent)

ARG.1: 13 residues within 4Å: Chain A: H.125, S.129, D.132, T.142, I.143, A.144 Chain C: G.145, D.146, D.147, T.148 Chain F: P.121, G.122, D.146 11 PLIP interactions: 5 interactions with chain A, 5 interactions with chain C, 1 interactions with chain F Hydrogen bonds: A:H.125, A:T.142, A:A.144, A:A.144, C:D.146, C:D.147, C:D.147, C:T.148 Salt bridges: A:H.125, C:D.146, F:D.146 ARG.2: 4 residues within 4Å: Chain A: G.145, D.146 Chain E: D.146 Chain F: H.125 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain E, 1 interactions with chain F pi-Cation interactions: B:H.125, F:H.125 Hydrogen bonds: A:G.145 Salt bridges: A:D.146, E:D.146 ARG.4: 14 residues within 4Å: Chain A: G.145, D.146, D.147, T.148 Chain B: H.125, A.128, S.129, D.132, T.142, I.143, A.144 Chain E: P.121, G.122, D.146 16 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A, 1 Ligand-Ligand interactions, 1 interactions with chain E Hydrophobic interactions: B:A.128 Hydrogen bonds: B:H.125, B:T.142, B:T.142, B:A.144, A:D.146, A:D.147, A:D.147, A:D.147, A:T.148, A:T.148, R.4 Salt bridges: B:H.125, A:D.146, A:D.147, E:D.146 ARG.5: 5 residues within 4Å: Chain B: G.145, D.146 Chain D: D.146 Chain E: H.125 Ligands: ARG.8 7 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain C, 2 interactions with chain D, 2 interactions with chain B, 1 interactions with chain E Hydrogen bonds: R.8, D:G.145, B:G.145 pi-Cation interactions: C:H.125, E:H.125 Salt bridges: D:D.146, B:D.146 ARG.7: 13 residues within 4Å: Chain A: P.121, G.122, D.146 Chain E: G.145, D.146, D.147, T.148 Chain F: H.125, S.129, D.132, T.142, I.143, A.144 14 PLIP interactions: 7 interactions with chain F, 6 interactions with chain E, 1 interactions with chain A, Hydrogen bonds: F:H.125, F:T.142, F:A.144, F:A.144, E:D.146, E:D.147, E:D.147, E:T.148, E:T.148 Water bridges: F:S.129, F:S.129 Salt bridges: F:H.125, E:D.146, A:D.146 ARG.8: 4 residues within 4Å: Chain A: H.125 Chain C: D.146 Chain F: D.146 Ligands: ARG.5 6 PLIP interactions: 1 interactions with chain D, 2 interactions with chain F, 1 interactions with chain A, 1 Ligand-Ligand interactions, 1 interactions with chain C pi-Cation interactions: D:H.125, A:H.125 Hydrogen bonds: F:G.145, R.5 Salt bridges: F:D.146, C:D.146 ARG.9: 14 residues within 4Å: Chain B: G.145, D.146, D.147, T.148 Chain C: H.125, A.128, S.129, D.132, T.142, I.143, A.144 Chain D: P.121, G.122, D.146 14 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain C, 1 interactions with chain D, 6 interactions with chain B Hydrogen bonds: R.9, C:H.125, C:D.132, C:T.142, C:A.144, B:D.146, B:D.147, B:D.147, B:T.148, B:T.148 Hydrophobic interactions: C:A.128 Salt bridges: C:H.125, D:D.146, B:D.146 ARG.11: 14 residues within 4Å: Chain C: P.121, G.122, D.146 Chain D: H.125, A.128, S.129, D.132, T.142, I.143, A.144 Chain F: G.145, D.146, D.147, T.148 15 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain D, 7 interactions with chain F, 1 interactions with chain C Hydrogen bonds: R.11, D:H.125, D:D.132, D:T.142, D:A.144, F:D.146, F:D.147, F:D.147, F:T.148, F:T.148 Hydrophobic interactions: D:A.128 Salt bridges: D:H.125, F:D.146, F:D.147, C:D.146 ARG.12: 14 residues within 4Å: Chain B: P.121, G.122, D.146 Chain D: G.145, D.146, D.147, T.148 Chain E: H.125, A.128, S.129, D.132, T.142, I.143, A.144 9 PLIP interactions: 4 interactions with chain E, 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: E:H.125, E:I.143, E:A.144, D:D.146, D:D.147 Salt bridges: E:H.125, D:D.146, D:D.147, B:D.146

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 6 residues within 4Å: Chain A: K.67, R.69, T.75 Chain D: V.66, K.67 Chain L: A.13 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.67 Salt bridges: A:R.69 ACT.6: 6 residues within 4Å: Chain B: R.18, A.19, Q.22, E.62, R.96, Y.126 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.126 Salt bridges: B:R.18, B:R.96

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain D: R.18, R.96, R.99, Y.126 Chain K: T.3 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.18, D:R.99, D:Y.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cherney, L.T. et al., The structure of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator and Co-repressor, L-arginine. J.Mol.Biol. (2009)

Release Date

2009-03-24

Peptides

Arginine repressor: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Arginine repressor

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