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Crystal structure of a NAD kinase from archaeoglobus fulgidus in complex with its substrate and product: insights into the catalysis of NAD kinase

Analyse Crystal structure of a NAD kinase from archaeoglobus fulgidus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SUW
Type: protein
Length: 996 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable inorganic POLYPHOSPHATE/ATP-NAD kinase
EC: 2.7.1.23
UniProt: O30297
Ligands: NAP
Pockets: 11 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Probable inorganic POLYPHOSPHATE/ATP-NAD kinase (EC 2.7.1.23)	protein	249	21% helix, 40% strand	O30297

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, D, B, C

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	621	0.87	0.92	64	empty
2	483	0.73	0.82	61	NAP
3	75	0.72	0.96	21	empty
4	460	0.72	0.82	49	NAP
5	74	0.71	0.96	19	empty

Interfaces

6 interfaces between chains.

C–D · 1254 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1251 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 1116 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 1087 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 214 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1SUW · Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with its… · the same entry in another collection · chain A against A, TM-score 1.00
O30297 · AlphaFold monomer V2.0 prediction for NAD kinase (O30297) · a predicted model of the same protein · chain A 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 O30297
Elsewhere: RCSB PDB 1SUW · PDBe 1SUW · UniProt O30297

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