Research workbench

Yeast apo RNA polymerase I*

Analyse Yeast apo RNA polymerase I* in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HLS
Type: protein
Length: 3,896 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase I subunit RPA190; DNA-directed RNA polymerase I subunit…
EC: 2.7.7.6
UniProt: P10964, P22138, P07703, P50106, P20434, P20435, P46669, P20436, P32529, P22139, P28000, P40422
Ligands: ZN
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 12 distinct chains · 29% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6)	protein	1431	39% helix, 12% strand	P10964
B	DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6)	protein	1163	24% helix, 24% strand	P22138
C	DNA-directed RNA polymerases I and III subunit RPAC1	protein	304	25% helix, 30% strand	P07703
D	DNA-directed RNA polymerase I subunit RPA14	protein	59	37% helix, 5% strand	P50106
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	214	35% helix, 22% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	100	41% helix, 14% strand	P20435
G	DNA-directed RNA polymerase I subunit RPA43	protein	176	7% helix, 40% strand	P46669
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	131	3% helix, 54% strand	P20436
I	DNA-directed RNA polymerase I subunit RPA12	protein	107	6% helix, 27% strand	P32529
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	69	39% helix, 1% strand	P22139
K	DNA-directed RNA polymerases I and III subunit RPAC2	protein	98	42% helix, 26% strand	P28000
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	44	0% helix, 30% strand	P40422

Ligands and binding sites

ZN · Zinc ion · metal · 7 copies · chains A, B, I, J, L

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	260	0.83	0.95	33	empty
2	1078	0.82	0.83	143	empty
3	1055	0.82	0.83	95	empty
4	1018	0.80	0.82	111	empty
5	116	0.77	0.96	21	empty

Interfaces

26 interfaces between chains.

A–B · 9200 Å² buried · 107 hydrogen bonds · protein-protein
A–E · 2834 Å² buried · 40 hydrogen bonds · protein-protein
A–F · 2270 Å² buried · 21 hydrogen bonds · protein-protein
B–J · 2060 Å² buried · 21 hydrogen bonds · protein-protein
C–K · 1939 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6HLS · Yeast apo RNA polymerase I* · the same entry in another collection · chain L against L, 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 P10964
Every structure of UniProt P22138
Every structure of UniProt P07703
Every structure of UniProt P50106
Every structure of UniProt P20434
Every structure of UniProt P20435
Every structure of UniProt P46669
Every structure of UniProt P20436
Every structure of UniProt P32529
Every structure of UniProt P22139
Every structure of UniProt P28000
Every structure of UniProt P40422
Elsewhere: RCSB PDB 6HLS · PDBe 6HLS · UniProt P10964 · UniProt P22138 · UniProt P07703 · UniProt P50106 · UniProt P20434 · UniProt P20435 · UniProt P46669 · UniProt P20436 · UniProt P32529 · UniProt P22139 · UniProt P28000 · UniProt P40422

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