MolNFT v1 · #173898 · protein + DNA

Structures of class II bacterial transcription complexes

7BEF · DNA-directed RNA polymerase subunit alpha: “Structures of class II bacterial transcription complexes”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #173898 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7BEF
Type: protein + DNA
Length: 4,073 residues
Chains: 9
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: P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579, Q48413
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 9 distinct chains · 38% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	305	27% helix, 25% strand	P0A7Z4
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	228	22% helix, 34% strand	P0A7Z4
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	29% helix, 19% strand	P0A8V2
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1362	37% helix, 14% strand	P0A8T7
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	90	72% helix, 0% strand	P0A800
F	RNA polymerase sigma factor rpod	protein	496	68% helix, 0% strand	P00579
G	Transcriptional activator rama	protein	106	63% helix, 0% strand	Q48413
T	Pmicf promoter template DNA	dna	73	—	—
N	Pmicf promoter non-template DNA	dna	73	—	—

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	714	0.84	0.88	73	empty
2	561	0.83	0.89	83	empty
3	927	0.83	0.85	72	empty
4	382	0.82	0.91	60	empty
5	1101	0.82	0.83	102	empty

Interfaces

21 interfaces between chains.

C–D · 8431 Å² buried · 86 hydrogen bonds · protein-protein
D–F · 3064 Å² buried · 17 hydrogen bonds · protein-protein
C–F · 2632 Å² buried · 17 hydrogen bonds · protein-protein
T–N · 2552 Å² buried · 184 hydrogen bonds · nucleic-nucleic
A–C · 1945 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

7BEF · Structures of class II bacterial transcription complexes · the same entry in another collection · chain N against N, TM-score 1.00
Q48413 · AlphaFold monomer V2.0 prediction for transcriptional activator rama (Q48413) · a predicted model of the same protein · chain G against A, TM-score 0.77

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 P0A7Z4
Every structure of UniProt P0A8V2
Every structure of UniProt P0A8T7
Every structure of UniProt P0A800
Every structure of UniProt P00579
Every structure of UniProt Q48413
Elsewhere: RCSB PDB 7BEF · PDBe 7BEF · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579 · UniProt Q48413

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