MolNFT v1 · #183911 · protein + DNA

Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA

7O73 · General transcription and DNA repair factor iih helicase…: “Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA”. Electron microscopy, 5 ligands (SF4, BEF, ADP), 20 pockets (best…

PDB: 7O73
Type: protein + DNA
Length: 9,010 residues
Chains: 30
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: General transcription and DNA repair factor iih helicase subunit xpd; General…
EC: 3.6.4.12, 2.7.7.6
UniProt: P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145
Ligands: SF4, BEF, ADP, ZN, MG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 30 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	General transcription and DNA repair factor iih helicase subunit xpd (EC 3.6.4.12)	protein	752	51% helix, 13% strand	P06839
1	General transcription and DNA repair factor iih subunit TFB1	protein	522	57% helix, 10% strand	P32776
2	General transcription and DNA repair factor iih subunit TFB2	protein	445	53% helix, 14% strand	Q02939
3	RNA polymerase II transcription factor B subunit 3	protein	131	47% helix, 10% strand	Q03290
4	General transcription and DNA repair factor iih subunit TFB4	protein	293	40% helix, 17% strand	Q12004
5	General transcription and DNA repair factor iih subunit TFB5	protein	65	48% helix, 25% strand	Q3E7C1
6	General transcription and DNA repair factor iih subunit SSL1	protein	356	31% helix, 21% strand	Q04673
7	General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12)	protein	615	39% helix, 18% strand	Q00578
A	DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6)	protein	1428	42% helix, 17% strand	P04050
B	DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6)	protein	1180	27% helix, 26% strand	P08518
C	DNA-directed RNA polymerase II subunit RPB3	protein	266	27% helix, 29% strand	P16370
D	DNA-directed RNA polymerase II subunit RPB4	protein	163	56% helix, 7% strand	P20433
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	214	40% helix, 23% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	86	35% helix, 16% strand	P20435
G	DNA-directed RNA polymerase II subunit RPB7	protein	171	13% helix, 51% strand	P34087
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	140	3% helix, 49% strand	P20436
I	DNA-directed RNA polymerase II subunit RPB9	protein	116	3% helix, 31% strand	P27999
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	69	42% helix, 4% strand	P22139
K	DNA-directed RNA polymerase II subunit RPB11	protein	115	39% helix, 23% strand	P38902
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	45	0% helix, 38% strand	P40422
M	Transcription initiation factor iib	protein	308	56% helix, 7% strand	P29055
N	Non-template DNA	dna	65	—	—
O	Tata-box-binding protein	protein	181	27% helix, 35% strand	P13393
Q	Transcription initiation factor iif subunit alpha	protein	221	29% helix, 26% strand	P41895
R	Transcription initiation factor iif subunit beta (EC 3.6.4.12)	protein	268	28% helix, 24% strand	P41896
T	Template DNA	dna	65	—	—
U	Transcription initiation factor iia large subunit	protein	107	39% helix, 36% strand	P32773
V	Transcription initiation factor iia subunit 2	protein	104	39% helix, 39% strand	P32774
W	Transcription initiation factor iie subunit alpha	protein	312	50% helix, 11% strand	P36100
X	Transcription initiation factor iie subunit beta	protein	207	40% helix, 11% strand	P36145

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains 0
BEF · Beryllium trifluoride ion · ligand · chains 7
ADP · Adenosine-5'-diphosphate · ligand · chains 7
ZN · Zinc ion · metal · 17 copies · chains 3, 4, 6, A, B, C, I, J, L, M, W
MG · Magnesium ion · metal · 2 copies · chains 7, 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	867	0.85	0.87	127	empty
2	971	0.84	0.85	101	empty
3	996	0.83	0.84	101	empty
4	223	0.83	0.96	36	empty
5	650	0.83	0.87	88	empty

Interfaces

96 interfaces between chains.

A–B · 10007 Å² buried · 130 hydrogen bonds · protein-protein
0–1 · 4211 Å² buried · 41 hydrogen bonds · protein-protein
Q–R · 3522 Å² buried · 69 hydrogen bonds · protein-protein
B–Q · 3053 Å² buried · 16 hydrogen bonds · protein-protein
1–4 · 3011 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

7O73 · Yeast RNA polymerase II transcription pre-initiation complex with closed distorted… · the same entry in another collection · chain C against C, 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 P06839
Every structure of UniProt P32776
Every structure of UniProt Q02939
Every structure of UniProt Q03290
Every structure of UniProt Q12004
Every structure of UniProt Q3E7C1
Every structure of UniProt Q04673
Every structure of UniProt Q00578
Every structure of UniProt P04050
Every structure of UniProt P08518
Every structure of UniProt P16370
Every structure of UniProt P20433
Every structure of UniProt P20434
Every structure of UniProt P20435
Every structure of UniProt P34087
Every structure of UniProt P20436
Every structure of UniProt P27999
Every structure of UniProt P22139
Every structure of UniProt P38902
Every structure of UniProt P40422
Every structure of UniProt P29055
Every structure of UniProt P13393
Every structure of UniProt P41895
Every structure of UniProt P41896
Every structure of UniProt P32773
Every structure of UniProt P32774
Every structure of UniProt P36100
Every structure of UniProt P36145
Elsewhere: RCSB PDB 7O73 · PDBe 7O73 · UniProt P06839 · UniProt P32776 · UniProt Q02939 · UniProt Q03290 · UniProt Q12004 · UniProt Q3E7C1 · UniProt Q04673 · UniProt Q00578 · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt P29055 · UniProt P13393 · UniProt P41895 · UniProt P41896 · UniProt P32773 · UniProt P32774 · UniProt P36100 · UniProt P36145

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.