MolNFT v1 · #109708 · protein

Crystal structure of ATS13 from actinomadura melliaura

4XAU · Putative aminotransferase: “Crystal structure of ATS13 from actinomadura melliaura”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.79). MolNFT v1 #109708 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4XAU
Type: protein
Length: 2,621 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative aminotransferase
UniProt: Q0H2X1
Ligands: PLP
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative aminotransferase	protein	372	39% helix, 17% strand	Q0H2X1
B, D	Putative aminotransferase	protein	378	38% helix, 16% strand	Q0H2X1
C	Putative aminotransferase	protein	374	39% helix, 16% strand	Q0H2X1
E, F, G	Putative aminotransferase	protein	373	40% helix, 17% strand	Q0H2X1

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · chains C, E

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	110	0.79	0.98	28	empty
2	99	0.77	0.97	26	empty
3	77	0.75	0.98	26	empty
4	348	0.72	0.84	51	PLP
5	304	0.72	0.85	43	empty

Interfaces

9 interfaces between chains.

D–F · 2540 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 2492 Å² buried · 33 hydrogen bonds · protein-protein
C–E · 2485 Å² buried · 35 hydrogen bonds · protein-protein
A–G · 372 Å² buried · 1 hydrogen bond · protein-protein
A–E · 203 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4XAU · Crystal structure of AtS13 from Actinomadura melliaura · the same entry in another collection · chain A against A, TM-score 1.00

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 Q0H2X1
Elsewhere: RCSB PDB 4XAU · PDBe 4XAU · UniProt Q0H2X1

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