MolNFT v1 · #163168 · protein + DNA

RNA polymerase I open complex conformation 1

6RUO · RNA polymerase I-specific transcription initiation factor…: “RNA polymerase I open complex conformation 1”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #163168 on GenesisL1: 3D structure…

PDB: 6RUO
Type: protein + DNA
Length: 6,179 residues
Chains: 20
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA polymerase I-specific transcription initiation factor RRN7; DNA-directed RNA…
EC: 2.7.7.6
UniProt: P40992, Q01080, P10964, P22138, P07703, P50106, P20434, P20435, P46669, P20436, P32529, P22139, P28000, P40422, P47006, P36070, P32786, Q04712
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 20 distinct chains · 29% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Q	RNA polymerase I-specific transcription initiation factor RRN7	protein	430	47% helix, 1% strand	P40992
M	DNA-directed RNA polymerase I subunit RPA49	protein	107	0% helix, 41% strand	Q01080
A	DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6)	protein	1465	35% helix, 12% strand	P10964
B	DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6)	protein	1180	22% helix, 19% strand	P22138
C	DNA-directed RNA polymerases I and III subunit RPAC1	protein	304	19% helix, 29% strand	P07703
D	DNA-directed RNA polymerase I subunit RPA14	protein	70	44% helix, 3% strand	P50106
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	215	30% helix, 23% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	100	37% helix, 15% strand	P20435
G	DNA-directed RNA polymerase I subunit RPA43	protein	199	10% helix, 35% strand	P46669
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	134	0% helix, 36% strand	P20436
I	DNA-directed RNA polymerase I subunit RPA12	protein	124	2% helix, 22% strand	P32529
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	69	33% helix, 4% strand	P22139
K	DNA-directed RNA polymerases I and III subunit RPAC2	protein	103	33% helix, 22% strand	P28000
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	45	0% helix, 18% strand	P40422
N	DNA-directed RNA polymerase I subunit RPA34	protein	139	3% helix, 18% strand	P47006
O	RNA polymerase I-specific transcription initiation factor RRN3	protein	462	49% helix, 0% strand	P36070
S	RNA polymerase I-specific transcription initiation factor RRN6	protein	610	18% helix, 24% strand	P32786
R	RNA polymerase I-specific transcription initiation factor RRN11	protein	330	49% helix, 1% strand	Q04712
T	Template strand	dna	50	—	—
U	Nontemplate strand	dna	43	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains Q, D, 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	1102	0.87	0.88	99	empty
2	828	0.85	0.88	115	empty
3	814	0.85	0.87	85	empty
4	570	0.84	0.89	56	empty
5	1162	0.83	0.84	108	empty

Interfaces

56 interfaces between chains.

A–B · 9126 Å² buried · 102 hydrogen bonds · protein-protein
S–R · 4143 Å² buried · 37 hydrogen bonds · protein-protein
Q–S · 4124 Å² buried · 26 hydrogen bonds · protein-protein
A–E · 2992 Å² buried · 36 hydrogen bonds · protein-protein
A–I · 2979 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

6RUO · RNA Polymerase I Open Complex conformation 1 · the same entry in another collection · chain H against H, 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 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
Every structure of UniProt P32786
Every structure of UniProt Q04712
Elsewhere: RCSB PDB 6RUO · PDBe 6RUO · UniProt P40992 · 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 · UniProt P32786 · UniProt Q04712

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