MolNFT v1 · #69977 · protein

Crystal structure of phosphate bound apo glyceraldehyde-3-phosphate dehydrogenase 1 from MRSA252 at 2.2 ångström resolution

3L6O: “Crystal structure of phosphate bound apo glyceraldehyde-3-phosphate dehydrogenase 1 from MRSA252 at 2.2…”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.80). MolNFT v1 #69977 on GenesisL1: 3D structure, binding…

PDB: 3L6O
Type: protein
Length: 1,335 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyceraldehyde-3-phosphate dehydrogenase 1
EC: 1.2.1.12
UniProt: Q6GIL8
Ligands: PO4
Pockets: 8 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Q, P, R	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12)	protein	334	26% helix, 28% strand	Q6GIL8
O	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12)	protein	333	28% helix, 29% strand	Q6GIL8

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains Q, P, R, O

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	990	0.80	0.82	106	PO4
2	778	0.75	0.80	116	empty
3	529	0.73	0.82	59	PO4
4	464	0.72	0.82	53	PO4
5	92	0.47	0.81	20	empty

Interfaces

6 interfaces between chains.

P–O · 2209 Å² buried · 41 hydrogen bonds · protein-protein
Q–R · 2188 Å² buried · 49 hydrogen bonds · protein-protein
Q–P · 1504 Å² buried · 30 hydrogen bonds · protein-protein
R–O · 1500 Å² buried · 29 hydrogen bonds · protein-protein
Q–O · 629 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3L6O · Crystal Structure of Phosphate bound apo Glyceraldehyde-3-phosphate dehydrogenase 1 from… · the same entry in another collection · chain O against O, TM-score 1.00
Q6GIL8 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase 1 (Q6GIL8) · a predicted model of the same protein · chain P 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 Q6GIL8
Elsewhere: RCSB PDB 3L6O · PDBe 3L6O · UniProt Q6GIL8

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