MolNFT v1 · #179875 · protein + DNA

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

7KIM · DNA-directed RNA polymerase subunit alpha: “Mycobacterium tuberculosis wt rnap transcription closed promoter complex with WHIB7 transcription factor”. Electron microscopy, 3 ligands (SF4, ZN, MG), 20 pockets (best druggability…

PDB: 7KIM
Type: protein + DNA
Length: 3,662 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 0.82

Structure

electron microscopy · 11 distinct chains · 35% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	225	19% helix, 32% strand	A5U8D3
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	237	19% helix, 31% strand	A5U8D3
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1111	24% helix, 22% strand	A5U052
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1270	43% helix, 12% strand	A0A045J9E2
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	83	45% helix, 5% strand	A0A0T9N9K3
F	RNA polymerase sigma factor siga	protein	322	68% helix, 2% strand	A0A0H3LGM9
J	RNA polymerase-binding protein rbpa	protein	109	23% helix, 23% strand	P9WHJ4
M	RNA polymerase-binding transcription factor card	protein	135	41% helix, 20% strand	P9WJG2
O	DNA (45-mer)	dna	45	—	—
P	DNA (45-mer)	dna	45	—	—
Z	Probable transcriptional regulator WHIB7	protein	80	30% helix, 5% 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	1008	0.82	0.83	110	empty
2	644	0.81	0.86	67	empty
3	1123	0.79	0.80	126	empty
4	869	0.77	0.80	64	empty
5	573	0.75	0.83	63	empty

Interfaces

25 interfaces between chains.

C–D · 8083 Å² buried · 69 hydrogen bonds · protein-protein
A–B · 2423 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 2202 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 2170 Å² buried · 28 hydrogen bonds · protein-protein
O–P · 2076 Å² buried · 200 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

7KIM · Mycobacterium tuberculosis WT RNAP transcription closed 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 0.97

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 7KIM · PDBe 7KIM · UniProt A5U8D3 · UniProt A5U052 · UniProt A0A045J9E2 · UniProt A0A0T9N9K3 · UniProt A0A0H3LGM9 · UniProt P9WHJ4 · UniProt P9WJG2 · UniProt Q6MX01

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