MolNFT v1 · #126540 · protein + DNA + RNA

RNA polymerase I elongation complex 2

5M5Y · DNA-directed RNA polymerase I subunit RPA190: “RNA polymerase I elongation complex 2”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.84). MolNFT v1 #126540 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5M5Y
Type: protein + DNA + RNA
Length: 4,212 residues
Chains: 17
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
Ligands: ZN
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 17 distinct chains · 29% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase I subunit RPA190 (EC 2.7.7.6)	protein	1466	40% helix, 10% strand	P10964
B	DNA-directed RNA polymerase I subunit RPA135 (EC 2.7.7.6)	protein	1170	24% helix, 21% strand	P22138
C	DNA-directed RNA polymerases I and III subunit RPAC1	protein	304	21% helix, 28% strand	P07703
D	DNA-directed RNA polymerase I subunit RPA14	protein	59	46% helix, 8% strand	P50106
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	214	39% helix, 24% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	100	43% helix, 11% strand	P20435
G	DNA-directed RNA polymerase I subunit RPA43	protein	202	10% helix, 38% strand	P46669
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	134	5% helix, 43% strand	P20436
I	DNA-directed RNA polymerase I subunit RPA12	protein	64	6% helix, 22% strand	P32529
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	69	38% helix, 0% strand	P22139
K	DNA-directed RNA polymerases I and III subunit RPAC2	protein	100	38% helix, 25% strand	P28000
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	43	0% helix, 28% strand	P40422
M	DNA-directed RNA polymerase I subunit RPA49	protein	101	0% helix, 36% strand	Q01080
N	DNA-directed RNA polymerase I subunit RPA34	protein	135	0% helix, 19% strand	P47006
R	RNA	rna	7	—	—
S	Non-template DNA	dna	19	—	—
T	Template DNA	dna	25	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, I, M, 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	822	0.84	0.86	105	empty
2	790	0.82	0.85	117	empty
3	1007	0.81	0.82	109	empty
4	509	0.81	0.88	58	empty
5	246	0.80	0.93	35	empty

Interfaces

40 interfaces between chains.

A–B · 9263 Å² buried · 91 hydrogen bonds · protein-protein
A–E · 2912 Å² buried · 45 hydrogen bonds · protein-protein
M–N · 2281 Å² buried · 27 hydrogen bonds · protein-protein
A–F · 2126 Å² buried · 20 hydrogen bonds · protein-protein
B–J · 2020 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

5M5Y · RNA Polymerase I elongation complex 2 · 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
Elsewhere: RCSB PDB 5M5Y · PDBe 5M5Y · 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

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