MolNFT v1 · #75079 · protein

Crystal structure of human NAD kinase

3PFN: “Crystal structure of human NAD kinase”. X-ray diffraction, 1 ligand (UNX), 16 pockets (best druggability 0.86). MolNFT v1 #75079 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3PFN
Type: protein
Length: 1,292 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD kinase
EC: 2.7.1.23
UniProt: O95544
Ligands: UNX
Pockets: 16 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 21% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD kinase (EC 2.7.1.23)	protein	327	22% helix, 35% strand	O95544
B	NAD kinase (EC 2.7.1.23)	protein	327	21% helix, 37% strand	O95544
C	NAD kinase (EC 2.7.1.23)	protein	321	20% helix, 38% strand	O95544
D	NAD kinase (EC 2.7.1.23)	protein	317	21% helix, 36% strand	O95544

Ligands and binding sites

UNX · Unknown atom or ion · ion · 62 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	919	0.86	0.88	62	UNX
2	918	0.75	0.78	81	UNX
3	799	0.72	0.77	77	UNX
4	598	0.72	0.80	77	UNX
5	744	0.70	0.77	57	UNX

Interfaces

6 interfaces between chains.

A–B · 3025 Å² buried · 45 hydrogen bonds · protein-protein
C–D · 2666 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 567 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 534 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 139 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 35 modified (engineered).

Compared structures

3PFN · Crystal Structure of human NAD kinase · the same entry in another collection · chain D against D, TM-score 1.00
O95544 · AlphaFold monomer V2.0 prediction for NAD kinase (O95544) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 O95544
Elsewhere: RCSB PDB 3PFN · PDBe 3PFN · UniProt O95544

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