Research workbench

Re-refinement of thermus thermopiles DNA-directed RNA polymerase structure

Analyse Re-refinement of thermus thermopiles DNA-directed RNA polymerase structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TMC
Type: protein
Length: 3,586 residues
Chains: 7
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: Q9Z9H6, Q8RQE9, Q8RQE8, Q72ID6, Q72L95
Ligands: G4P, MG, ZN, PO4
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 7 distinct chains · 28% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	231	20% helix, 33% strand	Q9Z9H6
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	238	18% helix, 29% strand	Q9Z9H6
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1119	21% helix, 23% strand	Q8RQE9
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1504	30% helix, 16% strand	Q8RQE8
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	95	40% helix, 6% strand	Q72ID6
F	RNA polymerase sigma factor siga	protein	351	55% helix, 1% strand	Q72L95
Z	Unknown protein	protein	48	23% helix, 0% strand	—

Ligands and binding sites

G4P · Guanosine-5',3'-tetraphosphate · ligand · chains C, D
MG · Magnesium ion · metal · 4 copies · chains C, D
ZN · Zinc ion · metal · 2 copies · chains D
PO4 · Phosphate ion · ion · chains A

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	895	0.86	0.88	96	empty
2	1185	0.86	0.87	121	empty
3	967	0.86	0.87	97	empty
4	670	0.83	0.87	93	MG
5	412	0.81	0.89	53	empty

Interfaces

11 interfaces between chains.

C–D · 8994 Å² buried · 109 hydrogen bonds · protein-protein
D–F · 4471 Å² buried · 61 hydrogen bonds · protein-protein
D–E · 2324 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 2043 Å² buried · 34 hydrogen bonds · protein-protein
C–F · 1965 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5TMC · Re-refinement of Thermus thermopiles DNA-directed RNA polymerase structure · the same entry in another collection · chain Z against Z, TM-score 1.00
Q9Z9H6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (Q9Z9H6) · a predicted model of the same protein · chain A against A, TM-score 0.96
Q72ID6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q72ID6) · a predicted model of the same protein · chain E against A, TM-score 0.94
Q72L95 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor siga (Q72L95) · a predicted model of the same protein · chain F against A, TM-score 0.86

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 Q9Z9H6
Every structure of UniProt Q8RQE9
Every structure of UniProt Q8RQE8
Every structure of UniProt Q72ID6
Every structure of UniProt Q72L95
Elsewhere: RCSB PDB 5TMC · PDBe 5TMC · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q72ID6 · UniProt Q72L95

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.