MolNFT v1 · #81490 · protein

Crystal structure of dava-4

3USF · Glutamate-1-semialdehyde 2,1-aminomutase: “Crystal structure of dava-4”. X-ray diffraction, 2 ligands (PLR, HOZ), 11 pockets (best druggability 0.82). MolNFT v1 #81490 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3USF
Type: protein
Length: 829 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate-1-semialdehyde 2,1-aminomutase
EC: 5.4.3.8
UniProt: Q31QJ2
Ligands: PLR, HOZ
Pockets: 11 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8)	protein	427	42% helix, 17% strand	Q31QJ2
B	Glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8)	protein	402	42% helix, 17% strand	Q31QJ2

Ligands and binding sites

PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
HOZ · (4S)-4,5-diaminopentanoic acid · ligand · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.82	0.97	36	PLR, HOZ
2	77	0.77	0.99	22	empty
3	71	0.76	0.99	22	empty
4	428	0.75	0.84	56	PLR
5	183	0.74	0.91	25	empty

Interfaces

1 interface between chains.

A–B · 4335 Å² buried · 55 hydrogen bonds · protein-protein

Compared structures

3USF · Crystal structure of DAVA-4 · the same entry in another collection · chain A against A, TM-score 1.00
Q31QJ2 · AlphaFold monomer V2.0 prediction for glutamate-1-semialdehyde 2,1-aminomutase (Q31QJ2) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q31QJ2
Elsewhere: RCSB PDB 3USF · PDBe 3USF · UniProt Q31QJ2

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