SMTL ID : 3lap.1

The Structure of the Intermediate Complex of the Arginine Repressor from Mycobacterium tuberculosis Bound to its DNA Operator and L-canavanine.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-hexamer

Ligands

6 x GGB: L-CANAVANINE(Non-covalent)

GGB.1: 14 residues within 4Å: Chain A: H.125, A.128, 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 18 PLIP interactions: 8 interactions with chain A, 1 interactions with chain F, 9 interactions with chain C Hydrophobic interactions: A:A.128 Hydrogen bonds: A:H.125, A:A.144, C:D.146, C:D.147, C:D.147, C:D.147, C:T.148, C:T.148 Water bridges: A:S.129, A:D.132, A:D.132, A:T.142, C:D.146, C:D.147 Salt bridges: A:H.125, F:D.146, C:D.146 GGB.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 19 PLIP interactions: 9 interactions with chain B, 9 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: B:A.128 Hydrogen bonds: B:H.125, B:A.144, A:D.146, A:D.147, A:D.147, A:D.147, A:T.148, A:T.148 Water bridges: B:S.129, B:D.132, B:D.132, B:R.133, B:T.142, A:D.146, A:D.147 Salt bridges: B:H.125, A:D.146, E:D.146 GGB.7: 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 18 PLIP interactions: 8 interactions with chain B, 9 interactions with chain C, 1 interactions with chain D Hydrogen bonds: B:D.146, B:D.147, B:D.147, B:T.148, B:T.148, C:H.125, C:D.132, C:A.144 Water bridges: B:D.146, B:D.147, C:S.129, C:D.132, C:D.132, C:T.142 Salt bridges: B:D.146, C:H.125, D:D.146 Hydrophobic interactions: C:A.128 GGB.10: 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: 8 interactions with chain F, 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: F:D.146, F:D.147, F:D.147, F:T.148, F:T.148, D:D.132, D:T.142, D:A.144 Water bridges: F:D.146, F:D.146, D:S.129, D:T.142 Salt bridges: F:D.146, C:D.146 Hydrophobic interactions: D:A.128 GGB.13: 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 16 PLIP interactions: 6 interactions with chain E, 9 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: E:A.128 Hydrogen bonds: E:D.132, E:T.142, E:A.144, D:D.146, D:D.147, D:D.147, D:T.148, D:T.148 Water bridges: E:S.129, E:T.142, D:D.146, D:D.146, D:D.147 Salt bridges: D:D.146, B:D.146 GGB.14: 14 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, A.128, S.129, D.132, T.142, I.143, A.144 16 PLIP interactions: 6 interactions with chain F, 9 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: F:A.128 Hydrogen bonds: F:D.132, F:T.142, F:A.144, E:D.146, E:D.147, E:D.147, E:T.148, E:T.148 Water bridges: F:S.129, F:T.142, E:D.146, E:D.146, E:D.147 Salt bridges: E:D.146, A:D.146

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

SO4.2: 5 residues within 4Å: Chain A: V.90, S.91, G.92, G.93, T.94 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.92, A:G.93, A:T.94 Water bridges: A:G.89, A:G.89 SO4.3: 3 residues within 4Å: Chain A: N.17, R.18, A.19 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.18, A:A.19, A:G.20 Water bridges: A:N.17, A:N.17 Salt bridges: A:R.18 SO4.5: 8 residues within 4Å: Chain B: K.67, R.69, T.75 Chain F: A.65, V.66, K.67, Y.78 Chain I: G.10 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain F Salt bridges: B:R.69 Hydrogen bonds: F:A.65, F:K.67, F:Y.78 SO4.6: 6 residues within 4Å: Chain B: A.16, N.17, R.18, A.19, G.20, S.91 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.17, B:N.17, B:A.19, B:G.20, B:S.91 SO4.8: 5 residues within 4Å: Chain C: N.17, R.18, A.19, G.20 Ligands: SO4.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.18, C:A.19, C:G.20 Salt bridges: C:R.18 SO4.9: 7 residues within 4Å: Chain C: A.16, N.17, A.19, G.20, R.21, S.91 Ligands: SO4.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.17, C:N.17, C:N.17, C:A.19, C:G.20, C:R.21, C:S.91 SO4.11: 5 residues within 4Å: Chain A: Q.33, R.35 Chain D: D.132, A.135 Chain F: R.118 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: D:D.132, A:R.35 Water bridges: D:L.136 Salt bridges: F:R.118 SO4.12: 6 residues within 4Å: Chain A: R.35, T.75, G.76 Chain D: A.135, L.136, P.137 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:A.135, A:T.75, A:G.76 Water bridges: D:R.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cherney, L.T. et al., crystal structure of the intermediate complex of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator reveals detailed mechanism of arginine repression. J.Mol.Biol. (2010)

Release Date

2010-05-05

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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