MolNFT v1 · #62105 · protein

Crystal structure and functional analysis of glyceraldehyde- 3-phosphate dehydrogenase from oryza sativa

3E5R · Glyceraldehyde-3-phosphate dehydrogenase, cytosolic: “Crystal structure and functional analysis of glyceraldehyde- 3-phosphate dehydrogenase from oryza sativa”. X-ray diffraction, 1 ligand (NAD), 10 pockets (best druggability 0.76).…

PDB: 3E5R
Type: protein
Length: 1,344 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyceraldehyde-3-phosphate dehydrogenase, cytosolic
EC: 1.2.1.12
UniProt: Q0J8A4
Ligands: NAD
Pockets: 10 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
O, A, B, C	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic (EC 1.2.1.12)	protein	336	31% helix, 27% strand	Q0J8A4

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, B, A, C

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1090	0.76	0.79	123	NAD
2	471	0.71	0.81	57	empty
3	417	0.69	0.81	49	empty
4	638	0.68	0.77	62	NAD
5	599	0.66	0.76	63	NAD

Interfaces

6 interfaces between chains.

A–B · 2016 Å² buried · 32 hydrogen bonds · protein-protein
O–C · 2006 Å² buried · 33 hydrogen bonds · protein-protein
O–B · 1421 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 1414 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 530 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3E5R · Crystal structure and Functional Analysis of Glyceraldehyde-3-phosphate Dehydrogenase… · the same entry in another collection · chain C against C, TM-score 1.00
Q0J8A4 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase 1… · a predicted model of the same protein · chain B against A, 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 Q0J8A4
Elsewhere: RCSB PDB 3E5R · PDBe 3E5R · UniProt Q0J8A4

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