Research workbench

Mycobacterium tuberculosis wt rnap transcription open promoter complex with WHIB7 transcription factor

Analyse Mycobacterium tuberculosis wt rnap transcription open promoter complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KIF
Type: protein + DNA
Length: 3,710 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
EC: 2.7.7.6
UniProt: A5U8D3, A5U052, A0A045J9E2, A0A0T9N9K3, A0A0H3LGM9, P9WHJ4, P9WJG2, Q6MX01
Ligands: SF4, ZN, MG
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 11 distinct chains · 35% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	225	18% helix, 36% strand	A5U8D3
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	237	18% helix, 32% strand	A5U8D3
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1111	24% helix, 23% strand	A5U052
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1270	42% helix, 13% strand	A0A045J9E2
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	83	43% helix, 5% strand	A0A0T9N9K3
F	RNA polymerase sigma factor siga	protein	322	67% helix, 1% strand	A0A0H3LGM9
J	RNA polymerase-binding protein rbpa	protein	109	23% helix, 22% strand	P9WHJ4
M	RNA polymerase-binding transcription factor card	protein	159	47% helix, 14% strand	P9WJG2
O	DNA (63-mer)	dna	63	—	—
P	DNA (55-mer)	dna	55	—	—
Z	Probable transcriptional regulator WHIB7	protein	76	33% helix, 3% strand	Q6MX01

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains F, Z
ZN · Zinc ion · metal · 2 copies · chains D
MG · Magnesium ion · metal · chains D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	892	0.81	0.84	74	empty
2	828	0.80	0.83	87	empty
3	785	0.76	0.81	81	empty
4	323	0.76	0.87	33	empty
5	481	0.75	0.83	52	empty

Interfaces

29 interfaces between chains.

C–D · 8303 Å² buried · 74 hydrogen bonds · protein-protein
O–P · 2446 Å² buried · 196 hydrogen bonds · nucleic-nucleic
D–F · 2434 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 2422 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 2195 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7KIF · Mycobacterium tuberculosis WT RNAP transcription open promoter complex with WhiB7… · the same entry in another collection · chain Z against Z, TM-score 1.00
A5U052 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (A5U052) · a predicted model of the same protein · chain C against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A5U8D3
Every structure of UniProt A5U052
Every structure of UniProt A0A045J9E2
Every structure of UniProt A0A0T9N9K3
Every structure of UniProt A0A0H3LGM9
Every structure of UniProt P9WHJ4
Every structure of UniProt P9WJG2
Every structure of UniProt Q6MX01
Elsewhere: RCSB PDB 7KIF · PDBe 7KIF · UniProt A5U8D3 · UniProt A5U052 · UniProt A0A045J9E2 · UniProt A0A0T9N9K3 · UniProt A0A0H3LGM9 · UniProt P9WHJ4 · UniProt P9WJG2 · UniProt Q6MX01

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