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Crystal structure of human bromodomain protein

Analyse Crystal structure of human bromodomain protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YYN
Type: protein
Length: 453 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription intermediary factor 1-alpha
UniProt: O15164
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 63% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Transcription intermediary factor 1-alpha	protein	113	64% helix, 0% strand	O15164
B	Transcription intermediary factor 1-alpha	protein	114	62% helix, 0% strand	O15164

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1137	0.80	0.82	80	empty
2	79	0.69	0.93	17	empty
3	238	0.60	0.80	35	empty
4	249	0.60	0.79	36	empty
5	54	0.44	0.84	15	empty

Interfaces

6 interfaces between chains.

A–B · 481 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 465 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 339 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 313 Å² buried · 1 hydrogen bond · protein-protein
A–C · 299 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2YYN · Crystal structure of human bromodomain protein · the same entry in another collection · chain A against A, TM-score 1.00
O15164 · AlphaFold monomer V2.0 prediction for transcription intermediary factor 1-alpha (O15164) · 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 O15164
Elsewhere: RCSB PDB 2YYN · PDBe 2YYN · UniProt O15164

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