MolNFT v1 · #191163 · protein

Human RNA polymerase I

8A43 · DNA-directed RNA polymerase I subunit RPA1: “Human RNA polymerase I”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #191163 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8A43
Type: protein
Length: 3,914 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase I subunit RPA1; DNA-directed RNA polymerase I subunit RPA2…
EC: 2.7.7.6
UniProt: O95602, Q9H9Y6, O15160, P19388, P61218, P52434, Q9P1U0, P62875, P0DPB6, P53803, Q9GZS1, O15446
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 12 distinct chains · 29% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase I subunit RPA1 (EC 2.7.7.6)	protein	1549	38% helix, 8% strand	O95602
B	DNA-directed RNA polymerase I subunit RPA2 (EC 2.7.7.6)	protein	1131	25% helix, 16% strand	Q9H9Y6
C	DNA-directed RNA polymerases I and III subunit RPAC1	protein	306	24% helix, 18% strand	O15160
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	209	35% helix, 15% strand	P19388
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	78	33% helix, 5% strand	P61218
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	148	3% helix, 41% strand	P52434
I	DNA-directed RNA polymerase I subunit RPA12	protein	47	0% helix, 4% strand	Q9P1U0
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	66	36% helix, 3% strand	P62875
K	DNA-directed RNA polymerases I and III subunit RPAC2	protein	107	44% helix, 20% strand	P0DPB6
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	46	0% helix, 15% strand	P53803
N	DNA-directed RNA polymerase I subunit RPA49	protein	105	7% helix, 43% strand	Q9GZS1
M	DNA-directed RNA polymerase I subunit RPA34	protein	122	7% helix, 30% strand	O15446

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	1018	0.87	0.88	84	empty
2	957	0.87	0.89	116	empty
3	844	0.82	0.84	65	empty
4	162	0.81	0.97	33	empty
5	1011	0.79	0.80	92	empty

Interfaces

22 interfaces between chains.

A–B · 8441 Å² buried · 71 hydrogen bonds · protein-protein
A–E · 3350 Å² buried · 38 hydrogen bonds · protein-protein
A–F · 2298 Å² buried · 27 hydrogen bonds · protein-protein
C–K · 1955 Å² buried · 4 hydrogen bonds · protein-protein
N–M · 1947 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

8A43 · Human RNA polymerase I · the same entry in another collection · chain M against M, TM-score 1.00

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 O95602
Every structure of UniProt Q9H9Y6
Every structure of UniProt O15160
Every structure of UniProt P19388
Every structure of UniProt P61218
Every structure of UniProt P52434
Every structure of UniProt Q9P1U0
Every structure of UniProt P62875
Every structure of UniProt P0DPB6
Every structure of UniProt P53803
Every structure of UniProt Q9GZS1
Every structure of UniProt O15446
Elsewhere: RCSB PDB 8A43 · PDBe 8A43 · UniProt O95602 · UniProt Q9H9Y6 · UniProt O15160 · UniProt P19388 · UniProt P61218 · UniProt P52434 · UniProt Q9P1U0 · UniProt P62875 · UniProt P0DPB6 · UniProt P53803 · UniProt Q9GZS1 · UniProt O15446

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