MolNFT v1 · #164731 · protein + DNA

Structure of human SOX2 transcription factor in complex with a nucleosome

6T7B · Histone H3.2: “Structure of human SOX2 transcription factor in complex with a nucleosome”. Electron microscopy, 20 pockets (best druggability 0.64). MolNFT v1 #164731 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6T7B
Type: protein + DNA
Length: 1,028 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-K; DNA (147-mer)…
UniProt: Q71DI3, P62805, P04908, O60814, P48431
Pockets: 20 · best druggability 0.64

Structure

electron microscopy · 9 distinct chains · 61% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H3.2	protein	98	62% helix, 4% strand	Q71DI3
B	Histone H4	protein	84	58% helix, 7% strand	P62805
C, G	Histone H2A type 1-B/E	protein	106	47% helix, 4% strand	P04908
D, H	Histone H2B type 1-K	protein	95	72% helix, 2% strand	O60814
E	Histone H3.2	protein	97	63% helix, 2% strand	Q71DI3
F	Histone H4	protein	81	60% helix, 5% strand	P62805
I	DNA (147-mer)	dna	95	—	—
J	DNA (147-mer)	dna	95	—	—
K	Transcription factor sox-2	protein	76	64% helix, 0% strand	P48431

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	778	0.64	0.74	83	empty
2	564	0.64	0.76	108	empty
3	302	0.61	0.80	34	empty
4	438	0.61	0.77	69	empty
5	241	0.60	0.81	28	empty

Interfaces

31 interfaces between chains.

I–J · 4181 Å² buried · 309 hydrogen bonds · nucleic-nucleic
C–D · 457 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 442 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 433 Å² buried · 4 hydrogen bonds · protein-protein
G–H · 420 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6T7B · Structure of human Sox2 transcription factor in complex with a nucleosome · the same entry in another collection · chain K against K, TM-score 1.00
Q71DI3 · AlphaFold monomer V2.0 prediction for histone H3.2 (Q71DI3) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q71DI3
Every structure of UniProt P62805
Every structure of UniProt P04908
Every structure of UniProt O60814
Every structure of UniProt P48431
Elsewhere: RCSB PDB 6T7B · PDBe 6T7B · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt O60814 · UniProt P48431

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