MolNFT v1 · #55881 · protein

Crystal structure of TT0281 from thermus thermophilus HB8

2YXZ · Thiamin-monophosphate kinase: “Crystal structure of TT0281 from thermus thermophilus HB8”. X-ray diffraction, 9 pockets (best druggability 0.75). MolNFT v1 #55881 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YXZ
Type: protein
Length: 1,219 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thiamin-monophosphate kinase
EC: 2.7.4.16
UniProt: Q5SL69
Pockets: 9 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Thiamin-monophosphate kinase (EC 2.7.4.16)	protein	305	36% helix, 27% strand	Q5SL69
D	Thiamin-monophosphate kinase (EC 2.7.4.16)	protein	304	37% helix, 26% strand	Q5SL69

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	502	0.75	0.83	55	empty
2	492	0.73	0.82	50	empty
3	482	0.73	0.82	65	empty
4	556	0.71	0.80	58	empty
5	278	0.56	0.77	42	empty

Interfaces

4 interfaces between chains.

A–C · 2818 Å² buried · 40 hydrogen bonds · protein-protein
B–D · 2558 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 141 Å² buried · 1 hydrogen bond · protein-protein
A–D · 77 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2YXZ · Crystal structure of tt0281 from Thermus thermophilus HB8 · 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 Q5SL69
Elsewhere: RCSB PDB 2YXZ · PDBe 2YXZ · UniProt Q5SL69

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