MolNFT v1 · #165278 · protein + DNA

Early intermediate RNA polymerase I pre-initiation complex - eipic

6TPS · DNA-directed RNA polymerase I subunit RPA190: “Early intermediate RNA polymerase I pre-initiation complex - eipic”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.87). MolNFT v1 #165278 on GenesisL1: 3D…

PDB: 6TPS
Type: protein + DNA
Length: 6,109 residues
Chains: 22
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, Q01080, P47006, P36070, P32786, P40992, Q04712
Ligands: ZN, MG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 22 distinct chains · 32% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6)	protein	1475	38% helix, 13% strand	P10964
B	DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6)	protein	1177	24% helix, 23% strand	P22138
C	DNA-directed RNA polymerases I and III subunit RPAC1	protein	305	19% helix, 32% strand	P07703
D	DNA-directed RNA polymerase I subunit RPA14	protein	58	47% helix, 10% strand	P50106
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	212	38% helix, 17% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	100	45% helix, 14% strand	P20435
G	DNA-directed RNA polymerase I subunit RPA43	protein	193	8% helix, 42% strand	P46669
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	131	2% helix, 52% strand	P20436
I	DNA-directed RNA polymerase I subunit RPA12	protein	73	10% helix, 18% strand	P32529
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	69	32% helix, 4% strand	P22139
K	DNA-directed RNA polymerases I and III subunit RPAC2	protein	101	37% helix, 30% strand	P28000
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	43	0% helix, 30% strand	P40422
M	DNA-directed RNA polymerase I subunit RPA49	protein	105	4% helix, 45% strand	Q01080
N	DNA-directed RNA polymerase I subunit RPA34	protein	145	0% helix, 26% strand	P47006
O	RNA polymerase I-specific transcription initiation factor RRN3	protein	463	57% helix, 0% strand	P36070
P	RNA polymerase I-specific transcription initiation factor RRN6	protein	595	21% helix, 28% strand	P32786
Q	RNA polymerase I-specific transcription initiation factor RRN7	protein	461	48% helix, 2% strand	P40992
R	RNA polymerase I-specific transcription initiation factor RRN11	protein	325	55% helix, 1% strand	Q04712
S	Nts-DNA (27-mer)	dna	27	—	—
T	Ts-DNA (27-mer)	dna	27	—	—
U	DNA foreign	dna	12	—	—
V	DNA foreign	dna	12	—	—

Ligands and binding sites

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

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	1168	0.87	0.88	115	empty
2	1105	0.83	0.84	108	empty
3	968	0.83	0.84	137	empty
4	686	0.82	0.86	93	empty
5	800	0.81	0.84	71	empty

Interfaces

55 interfaces between chains.

A–B · 9219 Å² buried · 99 hydrogen bonds · protein-protein
P–Q · 4087 Å² buried · 32 hydrogen bonds · protein-protein
P–R · 3280 Å² buried · 30 hydrogen bonds · protein-protein
A–E · 2895 Å² buried · 33 hydrogen bonds · protein-protein
M–N · 2393 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

6TPS · early intermediate RNA Polymerase I Pre-initiation complex - eiPIC · 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 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 Q01080
Every structure of UniProt P47006
Every structure of UniProt P36070
Every structure of UniProt P32786
Every structure of UniProt P40992
Every structure of UniProt Q04712
Elsewhere: RCSB PDB 6TPS · PDBe 6TPS · 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 Q01080 · UniProt P47006 · UniProt P36070 · UniProt P32786 · UniProt P40992 · UniProt Q04712

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