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Crystal structure of the brox BRO1 domain in complex with the C- terminal tail of CHMP5

Analyse Crystal structure of the brox BRO1 domain in complex with the C- terminal tail… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3UM2
Type: protein
Length: 784 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BRO1 domain-containing protein brox; Charged multivesicular body protein 5
UniProt: Q5VW32, Q9NZZ3
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	BRO1 domain-containing protein brox	protein	375	59% helix, 2% strand	Q5VW32
B, E	Charged multivesicular body protein 5	protein	17	0% helix, 24% strand	Q9NZZ3

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains A, D

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

Pockets

6 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	245	0.61	0.80	29	empty
2	228	0.57	0.79	31	empty
3	86	0.47	0.81	23	empty
4	89	0.36	0.75	17	empty
5	97	0.33	0.73	20	empty

Interfaces

6 interfaces between chains.

A–B · 504 Å² buried · 3 hydrogen bonds · protein-protein
D–E · 489 Å² buried · 3 hydrogen bonds · protein-protein
A–E · 220 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 214 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 133 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3UM2 · Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5 · the same entry in another collection · chain E against E, TM-score 1.00
Q5VW32 · AlphaFold monomer V2.0 prediction for BRO1 domain-containing protein brox (Q5VW32) · a predicted model of the same protein · chain A against A, TM-score 0.96
Q9NZZ3 · AlphaFold monomer V2.0 prediction for charged multivesicular body protein 5 (Q9NZZ3) · a predicted model of the same protein · chain B against A, TM-score 0.69

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 Q5VW32
Every structure of UniProt Q9NZZ3
Elsewhere: RCSB PDB 3UM2 · PDBe 3UM2 · UniProt Q5VW32 · UniProt Q9NZZ3

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