MolNFT v1 · #177365 · protein + DNA

Tfiid-based core pic on puma promoter

7EG8 · Transcription initiation factor tfiid subunit 1: “Tfiid-based core pic on puma promoter”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.89). MolNFT v1 #177365 on GenesisL1: 3D structure, binding sites and…

PDB: 7EG8
Type: protein + DNA
Length: 10,092 residues
Chains: 39
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription initiation factor tfiid subunit 1; Transcription initiation factor tfiid…
EC: 2.3.1.48, 2.7.11.1, 3.6.4.12, 2.7.7.6
UniProt: P21675, Q6P1X5, O00268, Q15542, P49848, Q15545, Q7Z7C8, Q16594, Q12962, Q16514, P52657, P20226, P52655, Q00403, P35269, P13984, Q5VWG9, Q15544, Q15543, A0A4X1TVZ5, I3LCH3, A0A481BYI6, I3LSI7, A0A4X1VEK9, A0A4X1VKG7, A0A4X1ULF2, P60899, A0A4X1UK25, A0A4X1TRS6
Ligands: ZN, MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 39 distinct chains · 35% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcription initiation factor tfiid subunit 1 (EC 2.3.1.48, 2.7.11.1)	protein	602	35% helix, 13% strand	P21675
B	Transcription initiation factor tfiid subunit 2	protein	963	40% helix, 20% strand	Q6P1X5
D	Transcription initiation factor tfiid subunit 4	protein	164	65% helix, 1% strand	O00268
E	Transcription initiation factor tfiid subunit 5	protein	546	22% helix, 29% strand	Q15542
F	Transcription initiation factor tfiid subunit 6	protein	404	57% helix, 2% strand	P49848
G	Transcription initiation factor tfiid subunit 7	protein	145	25% helix, 38% strand	Q15545
H	Transcription initiation factor tfiid subunit 8	protein	209	44% helix, 2% strand	Q7Z7C8
I	Transcription initiation factor tfiid subunit 9	protein	120	55% helix, 0% strand	Q16594
J	Transcription initiation factor tfiid subunit 10	protein	89	53% helix, 3% strand	Q12962
L	Transcription initiation factor tfiid subunit 12	protein	76	64% helix, 3% strand	Q16514
O	Transcription initiation factor iia subunit 2	protein	97	40% helix, 27% strand	P52657
P	Tata-box-binding protein	protein	177	28% helix, 34% strand	P20226
Q	Transcription initiation factor iia subunit 1	protein	122	43% helix, 32% strand	P52655
R	Transcription initiation factor iib (EC 2.3.1.48)	protein	251	55% helix, 3% strand	Q00403
S	General transcription factor iif subunit 1	protein	108	9% helix, 49% strand	P35269
T	General transcription factor iif subunit 2 (EC 3.6.4.12)	protein	222	28% helix, 30% strand	P13984
X	DNA (85-mer)	dna	85	—	—
Y	DNA (85-mer)	dna	85	—	—
c	Transcription initiation factor tfiid subunit 3	protein	127	53% helix, 3% strand	Q5VWG9
d	Transcription initiation factor tfiid subunit 4	protein	158	54% helix, 4% strand	O00268
e	Transcription initiation factor tfiid subunit 5	protein	539	13% helix, 26% strand	Q15542
f	Transcription initiation factor tfiid subunit 6	protein	403	55% helix, 4% strand	P49848
i	Transcription initiation factor tfiid subunit 9	protein	121	45% helix, 3% strand	Q16594
j	Transcription initiation factor tfiid subunit 10	protein	95	46% helix, 3% strand	Q12962
k	Transcription initiation factor tfiid subunit 11	protein	98	63% helix, 0% strand	Q15544
l	Transcription initiation factor tfiid subunit 12	protein	107	57% helix, 3% strand	Q16514
m	Transcription initiation factor tfiid subunit 13	protein	87	39% helix, 1% strand	Q15543
o	RPB1	protein	1427	36% helix, 14% strand	—
p	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1134	24% helix, 23% strand	A0A4X1TVZ5
q	DNA-directed RNA polymerase II subunit RPB3	protein	257	16% helix, 26% strand	I3LCH3
r	DNA-directed RNA polymerase II subunit RPB4	protein	128	52% helix, 2% strand	A0A481BYI6
s	DNA-directed RNA polymerase II subunit E	protein	209	33% helix, 20% strand	I3LSI7
t	DNA-directed RNA polymerase II subunit F	protein	79	35% helix, 19% strand	A0A4X1VEK9
u	DNA-directed RNA polymerase II subunit RPB7	protein	171	8% helix, 29% strand	A0A4X1VKG7
v	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	148	0% helix, 47% strand	A0A4X1ULF2
w	DNA-directed RNA polymerase II subunit RPB9	protein	114	7% helix, 27% strand	P60899
x	RPB10	protein	64	39% helix, 5% strand	—
y	RNA_POL_L_2 domain-containing protein	protein	117	38% helix, 19% strand	A0A4X1UK25
z	RPB12	protein	44	0% helix, 30% strand	A0A4X1TRS6

Ligands and binding sites

ZN · Zinc ion · metal · 9 copies · chains R, o, p, q, w, x, z
MG · Magnesium ion · metal · chains o

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	1194	0.89	0.91	134	empty
2	1161	0.87	0.88	131	empty
3	945	0.87	0.88	111	empty
4	1106	0.86	0.87	106	empty
5	1082	0.86	0.87	93	empty

Interfaces

113 interfaces between chains.

o–p · 8973 Å² buried · 91 hydrogen bonds · protein-protein
A–G · 5107 Å² buried · 79 hydrogen bonds · protein-protein
X–Y · 3919 Å² buried · 372 hydrogen bonds · nucleic-nucleic
O–Q · 2683 Å² buried · 39 hydrogen bonds · protein-protein
F–H · 2679 Å² buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7EG8 · TFIID-based core PIC on PUMA promoter · the same entry in another collection · chain O against O, 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 P21675
Every structure of UniProt Q6P1X5
Every structure of UniProt O00268
Every structure of UniProt Q15542
Every structure of UniProt P49848
Every structure of UniProt Q15545
Every structure of UniProt Q7Z7C8
Every structure of UniProt Q16594
Every structure of UniProt Q12962
Every structure of UniProt Q16514
Every structure of UniProt P52657
Every structure of UniProt P20226
Every structure of UniProt P52655
Every structure of UniProt Q00403
Every structure of UniProt P35269
Every structure of UniProt P13984
Every structure of UniProt Q5VWG9
Every structure of UniProt Q15544
Every structure of UniProt Q15543
Every structure of UniProt A0A4X1TVZ5
Every structure of UniProt I3LCH3
Every structure of UniProt A0A481BYI6
Every structure of UniProt I3LSI7
Every structure of UniProt A0A4X1VEK9
Every structure of UniProt A0A4X1VKG7
Every structure of UniProt A0A4X1ULF2
Every structure of UniProt P60899
Every structure of UniProt A0A4X1UK25
Every structure of UniProt A0A4X1TRS6
Elsewhere: RCSB PDB 7EG8 · PDBe 7EG8 · UniProt P21675 · UniProt Q6P1X5 · UniProt O00268 · UniProt Q15542 · UniProt P49848 · UniProt Q15545 · UniProt Q7Z7C8 · UniProt Q16594 · UniProt Q12962 · UniProt Q16514 · UniProt P52657 · UniProt P20226 · UniProt P52655 · UniProt Q00403 · UniProt P35269 · UniProt P13984 · UniProt Q5VWG9 · UniProt Q15544 · UniProt Q15543 · UniProt A0A4X1TVZ5 · UniProt I3LCH3 · UniProt A0A481BYI6 · UniProt I3LSI7 · UniProt A0A4X1VEK9 · UniProt A0A4X1VKG7 · UniProt A0A4X1ULF2 · UniProt P60899 · UniProt A0A4X1UK25 · UniProt A0A4X1TRS6

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