MolNFT v1 · #140123 · protein

Crystal structure of bacillus subtilis tmcal bound with alpha-thio ATP

5Y0P · UPF0348 protein B4417_3650: “Crystal structure of bacillus subtilis tmcal bound with alpha-thio ATP”. X-ray diffraction, 1 ligand (TAT), 8 pockets (best druggability 0.72). MolNFT v1 #140123 on GenesisL1: 3D structure, binding sites…

PDB: 5Y0P
Type: protein
Length: 802 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UPF0348 protein B4417_3650
UniProt: A0A164SIT4
Ligands: TAT
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	UPF0348 protein B4417_3650	protein	401	53% helix, 11% strand	A0A164SIT4

Ligands and binding sites

TAT · Adenosine-5'-rp-alpha-thio-triphosphate · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	326	0.72	0.85	44	TAT
2	311	0.70	0.84	32	TAT
3	588	0.69	0.78	77	empty
4	148	0.42	0.74	30	empty
5	162	0.39	0.73	25	empty

Interfaces

1 interface between chains.

A–B · 1139 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5Y0P · Crystal structure of Bacillus subtilis TmcAL bound with alpha-thio ATP · 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 A0A164SIT4
Elsewhere: RCSB PDB 5Y0P · PDBe 5Y0P · UniProt A0A164SIT4

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