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Crystal structure of glyceraldehyde-3-phosphate dehydrogenase complexed with nadfrom synechococcus elongatus"

Analyse Crystal structure of glyceraldehyde-3-phosphate dehydrogenase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3B20
Type: protein
Length: 2,027 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
EC: 1.2.1.13
UniProt: Q9R6W2
Ligands: NAD, SO4
Pockets: 11 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, P, Q, R	Glyceraldehyde 3-phosphate dehydrogenase (NADP+) (EC 1.2.1.13)	protein	338	30% helix, 27% strand	Q9R6W2
O	Glyceraldehyde 3-phosphate dehydrogenase (NADP+) (EC 1.2.1.13)	protein	337	30% helix, 27% strand	Q9R6W2

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, O, P, Q, R
SO4 · Sulfate ion · ion · 12 copies · chains A, B, O, P, Q, R

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	443	0.86	0.94	56	empty
2	734	0.72	0.78	65	SO4, NAD
3	551	0.72	0.80	57	SO4, NAD
4	668	0.70	0.78	62	SO4, NAD
5	487	0.69	0.80	54	SO4, NAD

Interfaces

7 interfaces between chains.

O–P · 1958 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 1951 Å² buried · 35 hydrogen bonds · protein-protein
Q–R · 1918 Å² buried · 36 hydrogen bonds · protein-protein
O–R · 1423 Å² buried · 15 hydrogen bonds · protein-protein
P–Q · 1403 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3B20 · Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with NADfrom… · the same entry in another collection · chain A 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 Q9R6W2
Elsewhere: RCSB PDB 3B20 · PDBe 3B20 · UniProt Q9R6W2

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