MolNFT v1 · #184199 · protein + DNA

Nucleosome with tbp and tfiia bound at shl +2

7OHA · Histone H3.2: “Nucleosome with tbp and tfiia bound at shl +2”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #184199 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7OHA
Type: protein + DNA
Length: 1,403 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (122-mer); Tata-binding…
UniProt: P84233, P62799, Q6AZJ8, P02281, G4XSG8, A0A6A5Q2T8, A0A6A5PRZ0
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 13 distinct chains · 53% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	97	66% helix, 4% strand	P84233
B	Histone H4	protein	82	60% helix, 9% strand	P62799
C	Histone H2A	protein	109	53% helix, 6% strand	Q6AZJ8
D	Histone H2B 1.1	protein	97	72% helix, 4% strand	P02281
E	Histone H3.2	protein	98	63% helix, 4% strand	P84233
F	Histone H4	protein	80	63% helix, 9% strand	P62799
G	Histone H2A	protein	106	58% helix, 7% strand	Q6AZJ8
H	Histone H2B 1.1	protein	95	75% helix, 4% strand	P02281
I	DNA (122-mer)	dna	122	—	—
J	DNA (122-mer)	dna	122	—	—
K	Tata-binding protein	protein	180	27% helix, 33% strand	G4XSG8
L	Transcription initiation factor iia large subunit	protein	108	37% helix, 31% strand	A0A6A5Q2T8
M	Transcription initiation factor iia subunit 2	protein	107	38% helix, 40% strand	A0A6A5PRZ0

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	941	0.82	0.84	102	empty
2	804	0.81	0.84	53	empty
3	425	0.76	0.85	44	empty
4	404	0.73	0.84	51	empty
5	237	0.72	0.88	38	empty

Interfaces

45 interfaces between chains.

I–J · 5476 Å² buried · 439 hydrogen bonds · nucleic-nucleic
L–M · 2811 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 2629 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 2622 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 2553 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

7OHA · nucleosome with TBP and TFIIA bound at SHL +2 · the same entry in another collection · chain M against M, 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 P84233
Every structure of UniProt P62799
Every structure of UniProt Q6AZJ8
Every structure of UniProt P02281
Every structure of UniProt G4XSG8
Every structure of UniProt A0A6A5Q2T8
Every structure of UniProt A0A6A5PRZ0
Elsewhere: RCSB PDB 7OHA · PDBe 7OHA · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt G4XSG8 · UniProt A0A6A5Q2T8 · UniProt A0A6A5PRZ0

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