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Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from borrelia burgdorferi

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

PDB: 3HJA
Type: protein
Length: 1,336 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyceraldehyde-3-phosphate dehydrogenase
EC: 1.2.1.12
UniProt: P46795
Ligands: NAD, SO4
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12)	protein	334	28% helix, 28% strand	P46795

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 12 copies · chains A, D, B, C

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

Pockets

8 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	853	0.78	0.81	97	empty
2	592	0.71	0.80	58	SO4, NAD
3	620	0.71	0.79	60	SO4, NAD
4	609	0.71	0.79	66	SO4, NAD
5	627	0.71	0.79	63	SO4, NAD

Interfaces

6 interfaces between chains.

B–C · 2011 Å² buried · 39 hydrogen bonds · protein-protein
A–D · 1983 Å² buried · 39 hydrogen bonds · protein-protein
C–D · 1418 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1406 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 498 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3HJA · Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Borrelia burgdorferi · the same entry in another collection · chain B against B, TM-score 1.00
P46795 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P46795) · 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 P46795
Elsewhere: RCSB PDB 3HJA · PDBe 3HJA · UniProt P46795

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