MolNFT v1 · #155973 · protein

Structural basis and functional analysis EPO1-BEM3P complex for bud growth

6LP3 · Uncharacterized protein YMR124W: “Structural basis and functional analysis EPO1-BEM3P complex for bud growth”. X-ray diffraction, 9 pockets (best druggability 0.78). MolNFT v1 #155973 on GenesisL1: 3D structure, binding sites and…

PDB: 6LP3
Type: protein
Length: 566 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein YMR124W; GTPase-activating protein BEM3
UniProt: P39523, P32873
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein YMR124W	protein	118	75% helix, 0% strand	P39523
B	Uncharacterized protein YMR124W	protein	120	81% helix, 0% strand	P39523
C, F	GTPase-activating protein BEM3	protein	43	93% helix, 0% strand	P32873
D	Uncharacterized protein YMR124W	protein	120	76% helix, 0% strand	P39523
E	Uncharacterized protein YMR124W	protein	122	81% helix, 0% strand	P39523

Pockets

9 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	705	0.78	0.83	97	empty
2	354	0.68	0.81	43	empty
3	388	0.63	0.78	55	empty
4	234	0.63	0.82	28	empty
5	133	0.44	0.76	19	empty

Interfaces

9 interfaces between chains.

D–E · 3662 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 3644 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 923 Å² buried · 5 hydrogen bonds · protein-protein
C–F · 915 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 822 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6LP3 · Structural basis and functional analysis epo1-bem3p complex for bud growth · the same entry in another collection · chain F against F, TM-score 1.00
P32873 · AlphaFold monomer V2.0 prediction for GTPase-activating protein BEM3 (P32873) · a predicted model of the same protein · chain C against A, TM-score 0.73
P39523 · AlphaFold monomer V2.0 prediction for uncharacterized protein YMR124W (P39523) · a predicted model of the same protein · chain A against A, TM-score 0.57

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 P39523
Every structure of UniProt P32873
Elsewhere: RCSB PDB 6LP3 · PDBe 6LP3 · UniProt P39523 · UniProt P32873

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