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PHGDH covalently linked to oridonin

Analyse PHGDH covalently linked to oridonin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DKM
Type: protein
Length: 612 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.7
Source: Homo sapiens
Molecule: D-3-phosphoglycerate dehydrogenase
EC: 1.1.1.95, 1.1.1.399, 1.1.1.37
UniProt: O43175
Ligands: NAD, ODN, NA, CL
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · resolution 1.7 · 1 distinct chain · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37)	protein	306	41% helix, 18% strand	O43175

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
ODN · (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14r, 16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one · ligand · chains A
NA · Sodium ion · metal · chains B
CL · Chloride ion · ion · 2 copies · chains A
1PE · Pentaethylene glycol · additive · chains B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	532	0.70	0.80	70	NAD
2	477	0.67	0.79	60	NAD
3	119	0.38	0.74	31	empty

Interfaces

1 interface between chains.

A–B · 2639 Å² buried · 52 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7DKM · Phgdh covalently linked to oridonin · the same entry in another collection · chain A against A, TM-score 1.00
O43175 · AlphaFold monomer V2.0 prediction for D-3-phosphoglycerate dehydrogenase (O43175) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O43175
Elsewhere: RCSB PDB 7DKM · PDBe 7DKM · UniProt O43175

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