Research workbench

P53-bound tfiid-based core pic on HDM2 promoter

Analyse P53-bound tfiid-based core pic on HDM2 promoter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EDX
Type: protein + DNA
Length: 9,991 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, A0A4X1VTX4, A0A4X1VEK9, A0A4X1ULF2, P60899, A0A4X1UK25, A0A4X1TRS6, A0A4X1VKG7
Ligands: ZN, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 39 distinct chains · 35% helix, 18% 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	33% 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	165	65% helix, 2% 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	21% helix, 34% 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	51% helix, 2% 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, 1% strand	Q16514
O	Transcription initiation factor iia subunit 2	protein	97	38% helix, 29% strand	P52657
P	Tata-box-binding protein	protein	177	28% helix, 34% strand	P20226
Q	Transcription initiation factor iia subunit 1	protein	122	40% helix, 32% strand	P52655
R	Transcription initiation factor iib (EC 2.3.1.48)	protein	248	55% helix, 4% strand	Q00403
S	General transcription factor iif subunit 1	protein	134	19% helix, 39% strand	P35269
T	General transcription factor iif subunit 2 (EC 3.6.4.12)	protein	113	16% helix, 49% strand	P13984
X	DNA (84-mer)	dna	77	—	—
Y	DNA (84-mer)	dna	77	—	—
c	Transcription initiation factor tfiid subunit 3	protein	127	53% helix, 3% strand	Q5VWG9
d	Transcription initiation factor tfiid subunit 4	protein	158	53% 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	54% 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	25% 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, 1% strand	A0A481BYI6
s	DNA-directed RNA polymerase II subunit E	protein	209	33% helix, 20% strand	A0A4X1VTX4
t	DNA-directed RNA polymerase II subunit F	protein	79	35% helix, 18% strand	A0A4X1VEK9
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, 3% 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
u	DNA-directed RNA polymerase II subunit RPB7	protein	171	10% helix, 52% strand	A0A4X1VKG7

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	1180	0.86	0.87	116	empty
2	1030	0.86	0.87	96	empty
3	1193	0.86	0.87	118	empty
4	832	0.86	0.88	96	empty
5	1071	0.85	0.86	129	empty

Interfaces

109 interfaces between chains.

o–p · 8108 Å² buried · 82 hydrogen bonds · protein-protein
A–G · 4954 Å² buried · 78 hydrogen bonds · protein-protein
X–Y · 3536 Å² buried · 354 hydrogen bonds · nucleic-nucleic
O–Q · 2646 Å² buried · 38 hydrogen bonds · protein-protein
c–j · 2643 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7EDX · p53-bound TFIID-based core PIC on HDM2 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 A0A4X1VTX4
Every structure of UniProt A0A4X1VEK9
Every structure of UniProt A0A4X1ULF2
Every structure of UniProt P60899
Every structure of UniProt A0A4X1UK25
Every structure of UniProt A0A4X1TRS6
Every structure of UniProt A0A4X1VKG7
Elsewhere: RCSB PDB 7EDX · PDBe 7EDX · 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 A0A4X1VTX4 · UniProt A0A4X1VEK9 · UniProt A0A4X1ULF2 · UniProt P60899 · UniProt A0A4X1UK25 · UniProt A0A4X1TRS6 · UniProt A0A4X1VKG7

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