MolNFT v1 · #23934 · protein

Crystal structure of TT1252 from thermus thermophilus

1UF9 · TT1252 protein: “Crystal structure of TT1252 from thermus thermophilus”. X-ray diffraction, 2 ligands (ATP, PO4), 7 pockets (best druggability 0.71). MolNFT v1 #23934 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1UF9
Type: protein
Length: 573 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TT1252 protein
UniProt: Q56416
Ligands: ATP, PO4
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	TT1252 protein	protein	191	54% helix, 14% strand	Q56416

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains C
PO4 · Phosphate ion · ion · chains B

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

Pockets

7 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	795	0.71	0.77	60	ATP
2	611	0.67	0.77	56	empty
3	325	0.62	0.78	32	empty
4	206	0.51	0.77	30	empty
5	91	0.39	0.77	15	empty

Interfaces

3 interfaces between chains.

A–C · 857 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 413 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 187 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 modified (engineered).

Compared structures

1UF9 · Crystal structure of TT1252 from Thermus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
Q56416 · AlphaFold monomer V2.0 prediction for dephospho-CoA kinase (Q56416) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 Q56416
Elsewhere: RCSB PDB 1UF9 · PDBe 1UF9 · UniProt Q56416

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