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Crystal structure of ligand-bound NAD1

Analyse Crystal structure of ligand-bound NAD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4CQK
Type: protein
Length: 658 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Flower-specific defensin
UniProt: Q8GTM0
Ligands: PIO, SO4
Pockets: 8 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N	Flower-specific defensin	protein	47	21% helix, 28% strand	Q8GTM0

Ligands and binding sites

PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 14 copies · chains A, C, G, J, B, H, D, N, E, F, K, I, L, M
SO4 · Sulfate ion · ion · 20 copies · chains A, C, G, D, J, B, N, E, F, I, K, H, L, M
MRD · (4R)-2-methylpentane-2,4-diol · additive · 4 copies · chains A, C, E, F, H, K

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	825	0.85	0.87	105	empty
2	549	0.80	0.87	71	empty
3	230	0.72	0.87	26	empty
4	50	0.58	0.91	19	empty
5	50	0.55	0.90	19	empty

Interfaces

25 interfaces between chains.

E–N · 471 Å² buried · 16 hydrogen bonds · protein-protein
D–G · 466 Å² buried · 16 hydrogen bonds · protein-protein
I–K · 465 Å² buried · 16 hydrogen bonds · protein-protein
F–H · 462 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 460 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 56 disulfide (disulfide).

Compared structures

4CQK · Crystal structure of ligand-bound NaD1 · the same entry in another collection · chain K against K, 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 Q8GTM0
Elsewhere: RCSB PDB 4CQK · PDBe 4CQK · UniProt Q8GTM0

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