Research workbench

Cryoem structure of sigma appropriation complex

Analyse Cryoem structure of sigma appropriation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6K4Y
Type: protein + DNA
Length: 4,055 residues
Chains: 10
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, P32267, P22915
Ligands: ZN, MG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 10 distinct chains · 37% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	219	21% helix, 34% strand	P0A7Z4
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	217	20% helix, 32% strand	P0A7Z4
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	29% helix, 22% strand	P0A8V2
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1335	36% helix, 17% strand	P0A8T7
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	79	61% helix, 0% strand	P0A800
F	RNA polymerase sigma factor rpod	protein	463	68% helix, 1% strand	P00579
I	10 kda anti-sigma factor	protein	88	68% helix, 0% strand	P32267
M	Middle transcription regulatory protein mota	protein	209	44% helix, 19% strand	P22915
N	DNA (60-mer)	dna	59	—	—
T	DNA (60-mer)	dna	46	—	—

Ligands and binding sites

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	1122	0.83	0.84	113	empty
2	836	0.82	0.85	68	empty
3	870	0.80	0.83	77	empty
4	316	0.79	0.90	43	empty
5	473	0.78	0.86	48	empty

Interfaces

25 interfaces between chains.

C–D · 8046 Å² buried · 74 hydrogen bonds · protein-protein
D–F · 2277 Å² buried · 30 hydrogen bonds · protein-protein
N–T · 2027 Å² buried · 202 hydrogen bonds · nucleic-nucleic
A–B · 1805 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 1780 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

6K4Y · CryoEM structure of sigma appropriation complex · the same entry in another collection · chain T against T, TM-score 1.00
P0A8V2 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V2) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P32267
Every structure of UniProt P22915
Elsewhere: RCSB PDB 6K4Y · PDBe 6K4Y · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579 · UniProt P32267 · UniProt P22915

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