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Pandda analysis group deposition -- crystal structure of BRD1 after initial refinement with no ligand modelled (structure 261)

Analyse Pandda analysis group deposition -- crystal structure of BRD1 after initial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5PWA
Type: protein
Length: 244 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 1
UniProt: O95696
Ligands: NA
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 1	protein	121	69% helix, 0% strand	O95696
B	Bromodomain-containing protein 1	protein	123	68% helix, 0% strand	O95696

Ligands and binding sites

NA · Sodium ion · metal · chains A, B
EDO · 1,2-ethanediol · additive · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	267	0.54	0.76	32	empty
2	99	0.50	0.82	18	EDO
3	79	0.50	0.83	17	EDO

Interfaces

1 interface between chains.

A–B · 550 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5PWA · PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement… · the same entry in another collection · chain A against A, TM-score 1.00
O95696 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 1 (O95696) · a predicted model of the same protein · chain B against A, TM-score 0.90

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Every structure of UniProt O95696
Elsewhere: RCSB PDB 5PWA · PDBe 5PWA · UniProt O95696

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