Research workbench

Schizosaccharomyces pombe RNA polymerase I (dimer)

Analyse Schizosaccharomyces pombe RNA polymerase I (dimer) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AOD
Type: protein
Length: 7,466 residues
Chains: 24
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase I subunit RPA1; Probable DNA-directed RNA polymerase I…
EC: 2.7.7.6
UniProt: P15398, Q9P7X8, O94616, Q9P7P1, Q09191, P36595, O43036, Q92399, O94703, O13877, Q09177, P48011
Ligands: ZN
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 12 distinct chains · 32% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, M	DNA-directed RNA polymerase I subunit RPA1 (EC 2.7.7.6)	protein	1384	43% helix, 12% strand	P15398
B, N	Probable DNA-directed RNA polymerase I subunit RPA2 (EC 2.7.7.6)	protein	1156	27% helix, 21% strand	Q9P7X8
C, O	DNA-directed RNA polymerases I and III subunit RPAC1	protein	317	25% helix, 31% strand	O94616
D, P	DNA-directed RNA polymerase I subunit RPA14	protein	39	69% helix, 0% strand	Q9P7P1
E, Q	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	207	25% helix, 18% strand	Q09191
F, R	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	82	29% helix, 10% strand	P36595
G, S	DNA-directed RNA polymerase I subunit RPA43	protein	160	9% helix, 40% strand	O43036
H, T	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	123	3% helix, 39% strand	Q92399
I, U	DNA-directed RNA polymerase I subunit RPA12	protein	57	7% helix, 16% strand	O94703
J, V	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	68	37% helix, 1% strand	O13877
K, W	DNA-directed RNA polymerases I and III subunit RPAC2	protein	95	39% helix, 20% strand	Q09177
L, X	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	45	0% helix, 31% strand	P48011

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, B, I, J, L, M, N, U, V, X

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	990	0.84	0.85	121	empty
2	1019	0.82	0.83	89	empty
3	1076	0.81	0.83	91	empty
4	512	0.80	0.87	73	empty
5	973	0.80	0.82	85	empty

Interfaces

64 interfaces between chains.

M–N · 9029 Å² buried · 91 hydrogen bonds · protein-protein
A–B · 8940 Å² buried · 95 hydrogen bonds · protein-protein
M–Q · 2494 Å² buried · 31 hydrogen bonds · protein-protein
A–E · 2493 Å² buried · 29 hydrogen bonds · protein-protein
M–R · 2089 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

7AOD · Schizosaccharomyces pombe RNA polymerase I (dimer) · the same entry in another collection · chain K against K, 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 P15398
Every structure of UniProt Q9P7X8
Every structure of UniProt O94616
Every structure of UniProt Q9P7P1
Every structure of UniProt Q09191
Every structure of UniProt P36595
Every structure of UniProt O43036
Every structure of UniProt Q92399
Every structure of UniProt O94703
Every structure of UniProt O13877
Every structure of UniProt Q09177
Every structure of UniProt P48011
Elsewhere: RCSB PDB 7AOD · PDBe 7AOD · UniProt P15398 · UniProt Q9P7X8 · UniProt O94616 · UniProt Q9P7P1 · UniProt Q09191 · UniProt P36595 · UniProt O43036 · UniProt Q92399 · UniProt O94703 · UniProt O13877 · UniProt Q09177 · UniProt P48011

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