MolNFT v1 · #184413 · protein + DNA + RNA

Pol II-csb-CRL4CSA-uvssa-SPT6-paf (structure 5)

7OPD · DNA-directed RNA polymerase II subunit RPB1: “Pol II-csb-CRL4CSA-uvssa-SPT6-paf (structure 5)”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.88). MolNFT v1 #184413 on GenesisL1: 3D structure, binding…

PDB: 7OPD
Type: protein + DNA + RNA
Length: 9,247 residues
Chains: 28
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase subunit beta…
EC: 2.7.7.6, 3.6.4.-, 2.3.2.27, 2.3.2.32
UniProt: P11414, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, F1SKN8, I3LJZ9, A0A4X1ULF2, P60899, A0A4X1VYD0, A0A4X1UK25, I3LN51, Q7KZ85, Q6PD62, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, Q13216, Q03468, Q2YD98, Q16531, Q13619, P62878
Ligands: ZN, MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 28 distinct chains · 36% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase II subunit RPB1	protein	1412	42% helix, 16% strand	P11414
B	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1131	29% helix, 25% strand	I3LGP4
C	DNA-directed RNA polymerase II subunit RPB3	protein	260	25% helix, 28% strand	I3LCH3
D	RPOL4C domain-containing protein	protein	128	63% helix, 3% strand	A0A287ADR4
E	DNA-directed RNA polymerase II subunit E	protein	209	42% helix, 25% strand	I3LSI7
F	DNA-directed RNA polymerase II subunit F	protein	82	33% helix, 16% strand	F1SKN8
G	DNA-directed RNA polymerase II subunit RPB7	protein	171	11% helix, 53% strand	I3LJZ9
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	148	5% helix, 49% strand	A0A4X1ULF2
I	DNA-directed RNA polymerase II subunit RPB9	protein	117	4% helix, 30% strand	P60899
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	67	42% helix, 4% strand	A0A4X1VYD0
K	RNA_POL_L_2 domain-containing protein	protein	115	42% helix, 23% strand	A0A4X1UK25
L	RNA polymerase II subunit K	protein	46	0% helix, 26% strand	I3LN51
M	Transcription elongation factor SPT6	protein	810	54% helix, 8% strand	Q7KZ85
N	Nts	dna	35	—	—
P	RNA	rna	21	—	—
R	LEO1 helix	protein	40	70% helix, 0% strand	—
S	RNA polymerase-associated protein CTR9 homolog	protein	890	70% helix, 1% strand	Q6PD62
T	Ts	dna	47	—	—
U	RNA polymerase-associated protein LEO1	protein	104	7% helix, 30% strand	Q8WVC0
V	RNA polymerase II-associated factor 1 homolog	protein	217	11% helix, 11% strand	Q8N7H5
Y	Wd repeat-containing protein 61	protein	300	0% helix, 51% strand	Q9GZS3
Z	Parafibromin	protein	43	60% helix, 2% strand	Q6P1J9
a	DNA excision repair protein ercc-8	protein	365	6% helix, 42% strand	Q13216
b	DNA excision repair protein ercc-6 (EC 3.6.4.-)	protein	520	46% helix, 10% strand	Q03468
c	UV-stimulated scaffold protein a	protein	141	69% helix, 0% strand	Q2YD98
d	DNA damage-binding protein 1	protein	1096	6% helix, 50% strand	Q16531
e	Cullin-4A	protein	711	59% helix, 4% strand	Q13619
f	E3 ubiquitin-protein ligase RBX1 (EC 2.3.2.27, 2.3.2.32)	protein	21	0% helix, 24% strand	P62878

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	806	0.88	0.92	115	empty
2	1082	0.87	0.88	126	empty
3	890	0.85	0.88	100	empty
4	422	0.85	0.94	45	empty
5	1196	0.85	0.86	157	empty

Interfaces

55 interfaces between chains.

A–B · 9101 Å² buried · 128 hydrogen bonds · protein-protein
a–d · 2523 Å² buried · 34 hydrogen bonds · protein-protein
A–E · 2414 Å² buried · 29 hydrogen bonds · protein-protein
C–K · 2285 Å² buried · 21 hydrogen bonds · protein-protein
A–H · 2162 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

7OPD · Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5) · 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 P11414
Every structure of UniProt I3LGP4
Every structure of UniProt I3LCH3
Every structure of UniProt A0A287ADR4
Every structure of UniProt I3LSI7
Every structure of UniProt F1SKN8
Every structure of UniProt I3LJZ9
Every structure of UniProt A0A4X1ULF2
Every structure of UniProt P60899
Every structure of UniProt A0A4X1VYD0
Every structure of UniProt A0A4X1UK25
Every structure of UniProt I3LN51
Every structure of UniProt Q7KZ85
Every structure of UniProt Q6PD62
Every structure of UniProt Q8WVC0
Every structure of UniProt Q8N7H5
Every structure of UniProt Q9GZS3
Every structure of UniProt Q6P1J9
Every structure of UniProt Q13216
Every structure of UniProt Q03468
Every structure of UniProt Q2YD98
Every structure of UniProt Q16531
Every structure of UniProt Q13619
Every structure of UniProt P62878
Elsewhere: RCSB PDB 7OPD · PDBe 7OPD · UniProt P11414 · UniProt I3LGP4 · UniProt I3LCH3 · UniProt A0A287ADR4 · UniProt I3LSI7 · UniProt F1SKN8 · UniProt I3LJZ9 · UniProt A0A4X1ULF2 · UniProt P60899 · UniProt A0A4X1VYD0 · UniProt A0A4X1UK25 · UniProt I3LN51 · UniProt Q7KZ85 · UniProt Q6PD62 · UniProt Q8WVC0 · UniProt Q8N7H5 · UniProt Q9GZS3 · UniProt Q6P1J9 · UniProt Q13216 · UniProt Q03468 · UniProt Q2YD98 · UniProt Q16531 · UniProt Q13619 · UniProt P62878

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