MolNFT v1 · #28929 · protein

Crystal structure of NAD kinase from thermotoga maritima

1YT5 · Inorganic POLYPHOSPHATE/ATP-NAD kinase: “Crystal structure of NAD kinase from thermotoga maritima”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.80). MolNFT v1 #28929 on GenesisL1: 3D structure, binding sites…

PDB: 1YT5
Type: protein
Length: 1,020 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inorganic POLYPHOSPHATE/ATP-NAD kinase
EC: 2.7.1.23
UniProt: Q9X255
Ligands: SO4
Pockets: 9 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Inorganic POLYPHOSPHATE/ATP-NAD kinase (EC 2.7.1.23)	protein	256	18% helix, 44% strand	Q9X255
C	Inorganic POLYPHOSPHATE/ATP-NAD kinase (EC 2.7.1.23)	protein	252	16% helix, 43% strand	Q9X255

Ligands and binding sites

SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D

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

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	1193	0.80	0.81	111	SO4
2	518	0.70	0.80	45	SO4
3	619	0.70	0.78	55	SO4
4	509	0.66	0.78	68	empty
5	137	0.64	0.87	32	empty

Interfaces

3 interfaces between chains.

B–C · 936 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 924 Å² buried · 1 hydrogen bond · protein-protein
A–C · 684 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1YT5 · Crystal structure of NAD kinase from Thermotoga maritima · the same entry in another collection · chain A against A, TM-score 1.00
Q9X255 · AlphaFold monomer V2.0 prediction for NAD kinase (Q9X255) · a predicted model of the same protein · chain C 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 Q9X255
Elsewhere: RCSB PDB 1YT5 · PDBe 1YT5 · UniProt Q9X255

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