Research workbench

The E. COLI class-II cap-dependent transcription activation complex at the state 2

Analyse The E. COLI class-II cap-dependent transcription activation complex at the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PB6
Type: protein + DNA
Length: 4,247 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: P0A7Z6, B7MIX3, P0A8T8, B7MFL0, P00579, P0ACK0
Ligands: CMP, ZN, MG
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 9 distinct chains · 37% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	230	23% helix, 31% strand	P0A7Z6
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	228	20% helix, 32% strand	P0A7Z6
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	31% helix, 21% strand	B7MIX3
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1337	35% helix, 13% strand	P0A8T8
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	79	65% helix, 0% strand	B7MFL0
F	RNA polymerase sigma factor rpod	protein	483	66% helix, 0% strand	P00579
G, H	Camp-activated global transcriptional regulator crp	protein	197	39% helix, 25% strand	P0ACK0
1	Synthetic nontemplate strand DNA (78-mer)	dna	78	—	—
2	Synthetic template strand DNA (78-mer)	dna	78	—	—

Ligands and binding sites

CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 2 copies · chains G, H
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	1070	0.90	0.91	145	empty
2	1130	0.89	0.91	163	empty
3	1134	0.88	0.89	145	empty
4	498	0.88	0.94	71	empty
5	1121	0.84	0.85	116	empty

Interfaces

24 interfaces between chains.

C–D · 7388 Å² buried · 82 hydrogen bonds · protein-protein
1–2 · 2837 Å² buried · 280 hydrogen bonds · nucleic-nucleic
D–F · 2158 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1679 Å² buried · 15 hydrogen bonds · protein-protein
C–F · 1588 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6PB6 · The E. coli class-II CAP-dependent transcription activation complex at the state 2 · the same entry in another collection · chain 2 against 2, TM-score 1.00
B7MIX3 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (B7MIX3) · a predicted model of the same protein · chain C against A, TM-score 0.96
P0A7Z6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (P0A7Z6) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 P0A7Z6
Every structure of UniProt B7MIX3
Every structure of UniProt P0A8T8
Every structure of UniProt B7MFL0
Every structure of UniProt P00579
Every structure of UniProt P0ACK0
Elsewhere: RCSB PDB 6PB6 · PDBe 6PB6 · UniProt P0A7Z6 · UniProt B7MIX3 · UniProt P0A8T8 · UniProt B7MFL0 · UniProt P00579 · UniProt P0ACK0

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