MolNFT v1 · #119090 · protein + DNA + RNA

Structure of transcribing mammalian RNA polymerase II

5FLM · DNA-directed RNA polymerase: “Structure of transcribing mammalian RNA polymerase II”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.88). MolNFT v1 #119090 on GenesisL1: 3D structure, binding sites and…

PDB: 5FLM
Type: protein + DNA + RNA
Length: 3,976 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase; DNA-directed RNA polymerase II subunit RPB2; DNA-directed…
EC: 2.7.7.6
UniProt: A5PJW8, Q3T0Q3, Q1JQ91, Q2T9T3, Q5E9B8, F2Z4H3, Q32P73, Q32P78, Q32P79, Q3ZBC0
Ligands: ZN, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 15 distinct chains · 32% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase (EC 2.7.7.6)	protein	1427	42% helix, 15% strand	—
B	DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6)	protein	1134	28% helix, 25% strand	A5PJW8
C	DNA-directed RNA polymerase II subunit RPB3	protein	257	23% helix, 26% strand	Q3T0Q3
D	DNA-directed RNA polymerase II subunit RPB4	protein	128	59% helix, 3% strand	Q1JQ91
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	209	39% helix, 20% strand	Q2T9T3
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	82	33% helix, 16% strand	—
G	DNA-directed RNA polymerase II subunit RPB7	protein	171	9% helix, 53% strand	Q5E9B8
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	148	3% helix, 47% strand	F2Z4H3
I	DNA-directed RNA polymerase II subunit RPB9	protein	114	7% helix, 30% strand	Q32P73
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	67	43% helix, 1% strand	Q32P78
K	DNA-directed RNA polymerase II subunit RPB11	protein	115	36% helix, 23% strand	Q32P79
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	44	0% helix, 30% strand	Q3ZBC0
N	DNA, DNA-RNA elongation scaffold	dna	27	—	—
P	RNA, DNA-RNA elongation scaffold	rna	14	—	—
T	DNA, DNA-RNA elongation scaffold	dna	39	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
MG · Magnesium ion · metal · chains A, P

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	970	0.88	0.90	127	empty
2	1193	0.88	0.89	127	empty
3	1045	0.84	0.85	97	empty
4	941	0.80	0.82	100	empty
5	489	0.79	0.86	65	empty

Interfaces

35 interfaces between chains.

A–B · 9483 Å² buried · 116 hydrogen bonds · protein-protein
A–E · 2443 Å² buried · 18 hydrogen bonds · protein-protein
A–F · 2261 Å² buried · 18 hydrogen bonds · protein-protein
C–K · 2258 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 2212 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

5FLM · Structure of transcribing mammalian RNA polymerase II · the same entry in another collection · chain T against T, 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 A5PJW8
Every structure of UniProt Q3T0Q3
Every structure of UniProt Q1JQ91
Every structure of UniProt Q2T9T3
Every structure of UniProt Q5E9B8
Every structure of UniProt F2Z4H3
Every structure of UniProt Q32P73
Every structure of UniProt Q32P78
Every structure of UniProt Q32P79
Every structure of UniProt Q3ZBC0
Elsewhere: RCSB PDB 5FLM · PDBe 5FLM · UniProt A5PJW8 · UniProt Q3T0Q3 · UniProt Q1JQ91 · UniProt Q2T9T3 · UniProt Q5E9B8 · UniProt F2Z4H3 · UniProt Q32P73 · UniProt Q32P78 · UniProt Q32P79 · UniProt Q3ZBC0

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