MolNFT v1 · #122451 · protein + DNA + RNA

Sigmas-transcription initiation complex with 4-nt nascent RNA

5IPL · DNA-directed RNA polymerase subunit alpha: “Sigmas-transcription initiation complex with 4-nt nascent RNA”. X-ray diffraction, 3 ligands (DPO, ZN, MG), 20 pockets (best druggability 0.85). MolNFT v1 #122451 on GenesisL1: 3D…

PDB: 5IPL
Type: protein + DNA + RNA
Length: 3,397 residues
Chains: 9
Method: x-ray diffraction
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, P13445
Ligands: DPO, ZN, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 9 distinct chains · 39% helix, 21% 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, 38% strand	P0A7Z4
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	228	24% helix, 39% strand	P0A7Z4
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	32% helix, 25% strand	P0A8V2
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1173	45% helix, 15% strand	P0A8T7
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	79	70% helix, 0% strand	P0A800
F	RNA polymerase sigma factor rpos	protein	277	68% helix, 2% strand	P13445
1	Synthetic nontemplate strand DNA (50-mer)	dna	33	—	—
2	Synthetic template strand DNA (50-mer)	dna	33	—	—
3	Nascent RNA 4-mer	rna	4	—	—

Ligands and binding sites

DPO · Diphosphate · ligand · chains C, D, 3
ZN · Zinc ion · metal · 2 copies · chains D
MG · Magnesium ion · metal · 2 copies · chains D, 3, C

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	925	0.85	0.87	85	empty
2	647	0.82	0.87	69	empty
3	606	0.82	0.88	69	empty
4	883	0.79	0.82	77	empty
5	290	0.79	0.91	46	empty

Interfaces

20 interfaces between chains.

C–D · 8440 Å² buried · 107 hydrogen bonds · protein-protein
D–F · 2738 Å² buried · 27 hydrogen bonds · protein-protein
C–F · 2518 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1935 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1785 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

5IPL · SigmaS-transcription initiation complex with 4-nt nascent RNA · the same entry in another collection · chain 3 against 3, 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 0.98
P13445 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor rpos (P13445) · a predicted model of the same protein · chain F against A, TM-score 0.97
P0A8T7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T7) · a predicted model of the same protein · chain D 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 P0A7Z4
Every structure of UniProt P0A8V2
Every structure of UniProt P0A8T7
Every structure of UniProt P0A800
Every structure of UniProt P13445
Elsewhere: RCSB PDB 5IPL · PDBe 5IPL · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P13445

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