MolNFT v1 · #163026 · protein + DNA

RNA polymerase I closed conformation 2 (CC2)

6RQL · Template strand: “RNA polymerase I closed conformation 2 (CC2)”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #163026 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6RQL
Type: protein + DNA
Length: 6,330 residues
Chains: 20
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Template strand; Nontemplate strand; RNA polymerase I-specific transcription initiation…
EC: 2.7.7.6
UniProt: P40992, P32786, Q04712, Q01080, P10964, P22138, P07703, P50106, P20434, P20435, P46669, P20436, P32529, P22139, P28000, P40422, P47006, P36070
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 20 distinct chains · 31% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	Template strand	dna	42	—	—
U	Nontemplate strand	dna	42	—	—
Q	RNA polymerase I-specific transcription initiation factor RRN7	protein	476	46% helix, 2% strand	P40992
S	RNA polymerase I-specific transcription initiation factor RRN6	protein	610	18% helix, 25% strand	P32786
R	RNA polymerase I-specific transcription initiation factor RRN11	protein	330	55% helix, 1% strand	Q04712
M	DNA-directed RNA polymerase I subunit RPA49	protein	107	4% helix, 45% strand	Q01080
A	DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6)	protein	1542	37% helix, 13% strand	P10964
B	DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6)	protein	1180	24% helix, 24% strand	P22138
C	DNA-directed RNA polymerases I and III subunit RPAC1	protein	304	22% helix, 30% strand	P07703
D	DNA-directed RNA polymerase I subunit RPA14	protein	70	53% helix, 7% strand	P50106
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	215	36% helix, 24% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	100	37% helix, 16% strand	P20435
G	DNA-directed RNA polymerase I subunit RPA43	protein	199	13% helix, 39% strand	P46669
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	134	4% helix, 47% strand	P20436
I	DNA-directed RNA polymerase I subunit RPA12	protein	124	3% helix, 21% strand	P32529
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	69	39% helix, 4% strand	P22139
K	DNA-directed RNA polymerases I and III subunit RPAC2	protein	103	37% helix, 22% strand	P28000
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	45	0% helix, 24% strand	P40422
N	DNA-directed RNA polymerase I subunit RPA34	protein	139	3% helix, 24% strand	P47006
O	RNA polymerase I-specific transcription initiation factor RRN3	protein	499	56% helix, 0% strand	P36070

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	897	0.86	0.88	86	empty
2	627	0.85	0.90	95	empty
3	746	0.83	0.87	79	empty
4	934	0.83	0.85	122	empty
5	960	0.82	0.84	88	empty

Interfaces

55 interfaces between chains.

A–B · 10065 Å² buried · 113 hydrogen bonds · protein-protein
S–R · 4326 Å² buried · 40 hydrogen bonds · protein-protein
Q–S · 4184 Å² buried · 22 hydrogen bonds · protein-protein
A–I · 2908 Å² buried · 30 hydrogen bonds · protein-protein
A–E · 2828 Å² buried · 41 hydrogen bonds · protein-protein

Compared structures

6RQL · RNA Polymerase I Closed Conformation 2 (CC2) · the same entry in another collection · chain C against C, 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 P40992
Every structure of UniProt P32786
Every structure of UniProt Q04712
Every structure of UniProt Q01080
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
Every structure of UniProt P47006
Every structure of UniProt P36070
Elsewhere: RCSB PDB 6RQL · PDBe 6RQL · UniProt P40992 · UniProt P32786 · UniProt Q04712 · UniProt Q01080 · UniProt P10964 · UniProt P22138 · UniProt P07703 · UniProt P50106 · UniProt P20434 · UniProt P20435 · UniProt P46669 · UniProt P20436 · UniProt P32529 · UniProt P22139 · UniProt P28000 · UniProt P40422 · UniProt P47006 · UniProt P36070

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