SMTL ID : 8cwr.1

Complex structure of WhiB3 and the SigmaAr4-RNAP Beta flap tip chimera in space group R3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-3-3-mer

Ligands

3 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 12 residues within 4Å: Chain A: G.21, C.23, F.31, C.53, C.56, V.58, I.59, C.62, V.75, G.77 Chain B: H.79, P.80 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.23, A:C.53, A:C.56, A:C.62 SF4.8: 12 residues within 4Å: Chain C: G.21, C.23, F.31, C.53, C.56, V.58, I.59, C.62, V.75, G.77 Chain D: H.79, P.80 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.23, C:C.53, C:C.56, C:C.62 SF4.15: 12 residues within 4Å: Chain E: G.21, C.23, F.31, C.53, C.56, V.58, I.59, C.62, V.75, G.77 Chain F: H.79, P.80 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.23, E:C.53, E:C.56, E:C.62

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

SO4.2: 4 residues within 4Å: Chain A: D.35, R.38, R.42 Chain B: R.65 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Water bridges: B:K.72, B:K.72, A:H.33, A:R.42, A:R.42, A:R.42 Salt bridges: B:R.65, A:R.38, A:R.42 SO4.3: 5 residues within 4Å: Chain B: H.4 Chain D: H.4 Chain F: H.4 Ligands: SO4.10, SO4.17 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B, 1 interactions with chain F Salt bridges: D:H.4, B:H.4, F:H.4 Water bridges: B:H.4 SO4.9: 4 residues within 4Å: Chain C: D.35, R.38, R.42 Chain D: R.65 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Water bridges: D:K.72, D:K.72, C:H.33, C:R.42, C:R.42, C:R.42 Salt bridges: D:R.65, C:R.38, C:R.42 SO4.10: 5 residues within 4Å: Chain B: H.4 Chain D: H.4 Chain F: H.4 Ligands: SO4.3, SO4.17 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 1 interactions with chain F Water bridges: D:H.4 Salt bridges: D:H.4, B:H.4, F:H.4 SO4.16: 4 residues within 4Å: Chain E: D.35, R.38, R.42 Chain F: R.65 9 PLIP interactions: 3 interactions with chain F, 6 interactions with chain E Water bridges: F:K.72, F:K.72, E:H.33, E:R.42, E:R.42, E:R.42 Salt bridges: F:R.65, E:R.38, E:R.42 SO4.17: 5 residues within 4Å: Chain B: H.4 Chain D: H.4 Chain F: H.4 Ligands: SO4.3, SO4.10 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 2 interactions with chain F Salt bridges: B:H.4, D:H.4, F:H.4 Water bridges: F:H.4

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 7 residues within 4Å: Chain B: H.3, E.100 Chain F: H.5, H.7, Q.20, L.44 Ligands: NI.6 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:Q.20, F:Q.20 Water bridges: B:E.100 TRS.11: 7 residues within 4Å: Chain B: H.5, H.7, Q.20, L.44 Chain D: H.3, E.100 Ligands: NI.13 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Water bridges: D:E.100 Hydrogen bonds: B:Q.20, B:Q.20 TRS.18: 7 residues within 4Å: Chain D: H.5, H.7, Q.20, L.44 Chain F: H.3, E.100 Ligands: NI.20 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D Water bridges: F:E.100 Hydrogen bonds: D:Q.20, D:Q.20

9 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 4 residues within 4Å: Chain B: A.2, H.3, H.4, H.5 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.4, H2O.4 NI.6: 4 residues within 4Å: Chain B: H.3 Chain F: H.5, H.7 Ligands: TRS.4 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Metal complexes: F:H.5, F:H.7, B:H.3 NI.7: 8 residues within 4Å: Chain B: H.6, H.8 Chain D: H.6, H.8 Chain F: H.6, H.8 Ligands: NI.14, NI.21 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 interactions with chain F Metal complexes: B:H.6, B:H.8, D:H.6, D:H.8, F:H.6, F:H.8 NI.12: 4 residues within 4Å: Chain D: A.2, H.3, H.4, H.5 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.4, H2O.8 NI.13: 4 residues within 4Å: Chain B: H.5, H.7 Chain D: H.3 Ligands: TRS.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Metal complexes: B:H.5, B:H.7, D:H.3 NI.14: 8 residues within 4Å: Chain B: H.6, H.8 Chain D: H.6, H.8 Chain F: H.6, H.8 Ligands: NI.7, NI.21 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 interactions with chain F Metal complexes: B:H.6, B:H.8, D:H.6, D:H.8, F:H.6, F:H.8 NI.19: 4 residues within 4Å: Chain F: A.2, H.3, H.4, H.5 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.4, H2O.12 NI.20: 4 residues within 4Å: Chain D: H.5, H.7 Chain F: H.3 Ligands: TRS.18 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Metal complexes: D:H.5, D:H.7, F:H.3 NI.21: 8 residues within 4Å: Chain B: H.6, H.8 Chain D: H.6, H.8 Chain F: H.6, H.8 Ligands: NI.7, NI.14 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F, 2 interactions with chain B Metal complexes: D:H.6, D:H.8, F:H.6, F:H.8, B:H.6, B:H.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wan, T. et al., Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis. J.Biol.Chem. (2023)

Release Date

2023-05-17

Peptides

Redox- and pH-responsive transcriptional regulator WhiB3: ACE
RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Redox- and pH-responsive transcriptional regulator WhiB3

RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta

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