SMTL ID : 8cwt.1

Complex structure of WhiB3 and the SigmaAr4-RNAP Beta flap tip chimera in space group P43212

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 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, M.52, C.53, C.56, 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 SF4.15: 12 residues within 4Å: Chain C: G.21, C.23, F.31, M.52, C.53, C.56, 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 SF4.28: 12 residues within 4Å: Chain E: G.21, C.23, F.31, M.52, C.53, C.56, 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

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

SO4.2: 3 residues within 4Å: Chain A: Q.47, K.50, R.54 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: P.34, D.35, G.36, E.37, R.38, R.42 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain A: H.33, R.42, E.46, S.80, E.81, S.82 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain B: R.41, T.51, L.52, R.63 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain B: H.5, Q.20 Chain F: A.2, H.4 Ligands: SO4.25 Ligand excluded by PLIP SO4.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: D.35 Chain B: R.33, V.61, R.65 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: L.19, R.24 Chain B: Q.84, R.87 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain B: S.31, E.32 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain C: D.35, G.36, R.38 Chain D: R.65 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain C: R.42, S.80, E.81, S.82 Ligands: SO4.18 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain C: H.33, R.42, P.72, Y.73, G.74, E.81 Ligands: SO4.17 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain B: A.2, H.4 Chain D: H.5, Q.20 Ligands: SO4.25 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain D: R.41, T.51, L.52, R.63 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: D.35 Chain D: R.33, R.65 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain D: S.31, E.32 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain B: H.4 Chain D: H.4 Chain F: H.4 Ligands: SO4.9, SO4.21, SO4.34 Ligand excluded by PLIP SO4.26: 1 residues within 4Å: Chain D: R.63 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain E: L.19, R.24 Chain F: Q.84, R.87 Ligand excluded by PLIP SO4.30: 1 residues within 4Å: Chain E: R.40 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain E: D.35, G.36, R.38 Chain F: R.65 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain D: A.2, H.4 Chain F: H.5, Q.20 Ligands: SO4.25 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain F: R.41, T.51, L.52, R.63 Ligand excluded by PLIP SO4.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain E: D.35 Chain F: R.33, V.61, R.65 Ligand excluded by PLIP

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

NI.5: 6 residues within 4Å: Chain B: H.6, H.8 Chain D: H.6, H.8 Chain F: H.6, H.8 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.6: 5 residues within 4Å: Chain B: H.5, H.7 Chain F: H.3, E.100 Ligands: TRS.38 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain B Metal complexes: F:H.3, B:H.5, B:H.7 NI.7: 5 residues within 4Å: Chain B: A.2, H.3, H.4, H.5 Chain D: H.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.4 NI.19: 5 residues within 4Å: Chain D: A.2, H.3, H.4, H.5 Chain F: H.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.4 NI.20: 5 residues within 4Å: Chain B: H.3, E.100 Chain D: H.5, H.7 Ligands: TRS.14 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Metal complexes: D:H.5, D:H.7, B:H.3 NI.32: 5 residues within 4Å: Chain D: H.3, E.100 Chain F: H.5, H.7 Ligands: TRS.27 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D Metal complexes: F:H.5, F:H.7, D:H.3 NI.33: 5 residues within 4Å: Chain B: H.5 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.20

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

TRS.14: 9 residues within 4Å: Chain B: H.3, P.99, E.100 Chain D: H.5, H.7, Q.20, L.23, L.44 Ligands: NI.20 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Water bridges: D:Q.20, D:L.44, B:E.100 TRS.27: 9 residues within 4Å: Chain D: H.3, P.99, E.100 Chain F: H.5, H.7, Q.20, L.23, L.44 Ligands: NI.32 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:L.44 TRS.38: 9 residues within 4Å: Chain B: H.5, H.7, Q.20, L.23, L.44 Chain F: H.3, P.99, E.100 Ligands: NI.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:L.44 Water bridges: B:Q.20, F:E.100

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
C

E
E

B
B

D
D

F
F

Redox- and pH-responsive transcriptional regulator WhiB3

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

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