MolNFT v1 · #148351 · protein + DNA

RNA polymerase III closed complex CC2.

6F44 · DNA-directed RNA polymerase III subunit RPC1: “RNA polymerase III closed complex CC2.”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #148351 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6F44
Type: protein + DNA
Length: 5,551 residues
Chains: 22
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase III subunit RPC1; DNA-directed RNA polymerase III subunit…
EC: 2.7.7.6
UniProt: P04051, P22276, P07703, P47076, P20434, P20435, P35718, P20436, Q04307, P22139, P28000, P40422, P36121, P25441, P32349, P32910, P17890, P13393, P29056, P46678
Ligands: ZN
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 22 distinct chains · 32% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase III subunit RPC1 (EC 2.7.7.6)	protein	1399	35% helix, 12% strand	P04051
B	DNA-directed RNA polymerase III subunit RPC2 (EC 2.7.7.6)	protein	1114	24% helix, 21% strand	P22276
C	DNA-directed RNA polymerases I and III subunit RPAC1	protein	335	17% helix, 28% strand	P07703
D	DNA-directed RNA polymerase III subunit RPC9	protein	119	39% helix, 3% strand	P47076
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	214	30% helix, 21% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	83	30% helix, 13% strand	P20435
G	DNA-directed RNA polymerase III subunit RPC8	protein	180	11% helix, 31% strand	P35718
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	140	0% helix, 46% strand	P20436
I	DNA-directed RNA polymerase III subunit RPC10	protein	34	9% helix, 21% strand	Q04307
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	67	48% helix, 3% strand	P22139
K	DNA-directed RNA polymerases I and III subunit RPAC2	protein	101	44% helix, 22% strand	P28000
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	45	0% helix, 22% strand	P40422
M	DNA-directed RNA polymerase III subunit RPC5	protein	171	21% helix, 30% strand	P36121
N	DNA-directed RNA polymerase III subunit RPC4	protein	104	19% helix, 35% strand	P25441
O	DNA-directed RNA polymerase III subunit RPC3	protein	534	52% helix, 5% strand	P32349
P	DNA-directed RNA polymerase III subunit RPC6	protein	99	36% helix, 9% strand	P32910
Q	DNA-directed RNA polymerase III subunit RPC7	protein	35	51% helix, 3% strand	P17890
U	Tata-box-binding protein	protein	180	21% helix, 26% strand	P13393
V	Transcription factor iiib 70 kda subunit	protein	337	48% helix, 3% strand	P29056
W	Transcription factor tfiiib component B''	protein	172	56% helix, 2% strand	P46678
X	Non-template DNA	dna	44	—	—
Y	Template DNA	dna	44	—	—

Ligands and binding sites

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

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	1024	0.86	0.87	94	empty
2	1161	0.84	0.85	98	empty
3	663	0.84	0.88	77	empty
4	917	0.83	0.84	92	empty
5	211	0.82	0.95	43	empty

Interfaces

56 interfaces between chains.

A–B · 8469 Å² buried · 75 hydrogen bonds · protein-protein
A–O · 2861 Å² buried · 28 hydrogen bonds · protein-protein
U–V · 2676 Å² buried · 19 hydrogen bonds · protein-protein
M–N · 2295 Å² buried · 38 hydrogen bonds · protein-protein
A–H · 2254 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6F44 · RNA Polymerase III closed complex CC2. · 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 P04051
Every structure of UniProt P22276
Every structure of UniProt P07703
Every structure of UniProt P47076
Every structure of UniProt P20434
Every structure of UniProt P20435
Every structure of UniProt P35718
Every structure of UniProt P20436
Every structure of UniProt Q04307
Every structure of UniProt P22139
Every structure of UniProt P28000
Every structure of UniProt P40422
Every structure of UniProt P36121
Every structure of UniProt P25441
Every structure of UniProt P32349
Every structure of UniProt P32910
Every structure of UniProt P17890
Every structure of UniProt P13393
Every structure of UniProt P29056
Every structure of UniProt P46678
Elsewhere: RCSB PDB 6F44 · PDBe 6F44 · UniProt P04051 · UniProt P22276 · UniProt P07703 · UniProt P47076 · UniProt P20434 · UniProt P20435 · UniProt P35718 · UniProt P20436 · UniProt Q04307 · UniProt P22139 · UniProt P28000 · UniProt P40422 · UniProt P36121 · UniProt P25441 · UniProt P32349 · UniProt P32910 · UniProt P17890 · UniProt P13393 · UniProt P29056 · UniProt P46678

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