MolNFT v1 · #16437 · protein

Shikimate dehydrogenase aroe complexed with NADP+

1NYT · Shikimate 5-dehydrogenase: “Shikimate dehydrogenase aroe complexed with NADP+”. X-ray diffraction, 3 ligands (NAP, DTV, SO4), 15 pockets (best druggability 0.89). MolNFT v1 #16437 on GenesisL1: 3D structure, binding sites and…

PDB: 1NYT
Type: protein
Length: 1,081 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Shikimate 5-dehydrogenase
EC: 1.1.1.25
UniProt: P15770
Ligands: NAP, DTV, SO4
Pockets: 15 · best druggability 0.89

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Shikimate 5-dehydrogenase (EC 1.1.1.25)	protein	271	43% helix, 18% strand	P15770
C	Shikimate 5-dehydrogenase (EC 1.1.1.25)	protein	269	41% helix, 18% strand	P15770
D	Shikimate 5-dehydrogenase (EC 1.1.1.25)	protein	270	40% helix, 18% strand	P15770

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
DTV · (2S,3S)-1,4-dimercaptobutane-2,3-diol · ligand · chains A
SO4 · Sulfate ion · ion · 14 copies · chains A, C, B, D

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

Pockets

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1173	0.89	0.90	129	empty
2	574	0.76	0.83	52	SO4, NAP
3	538	0.74	0.82	52	SO4, NAP, DTV
4	603	0.71	0.79	54	SO4, NAP
5	601	0.70	0.78	54	SO4, NAP

Interfaces

5 interfaces between chains.

B–D · 821 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 772 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 430 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 390 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 357 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1NYT · SHIKIMATE DEHYDROGENASE AroE COMPLEXED WITH NADP+ · the same entry in another collection · chain D against D, TM-score 1.00
P15770 · AlphaFold monomer V2.0 prediction for shikimate dehydrogenase (NADP(+)) (P15770) · 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 P15770
Elsewhere: RCSB PDB 1NYT · PDBe 1NYT · UniProt P15770

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