MolNFT v1 · #31744 · protein
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from plasmodium falciparum at 2.25 ångström resolution reveals intriguing extra electron density in the active site
2B4T: “Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from plasmodium falciparum at 2.25 ångström…”. X-ray diffraction, 2 ligands (NAD, AES), 11 pockets (best druggability 0.80). MolNFT v1 #31744 on GenesisL1: 3D structure…
- PDB
- 2B4T
- Type
- protein
- Length
- 1,332 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
- Q8T6B1
- Ligands
- NAD, AES
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, P, Q, R | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 333 | 30% helix, 27% strand | Q8T6B1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains O, R, P, Q
- AES · 4-(2-aminoethyl)benzenesulfonyl fluoride · ligand · 3 copies · chains O, P, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.80 | 0.81 | 109 | NAD, AES |
| 2 | 739 | 0.80 | 0.84 | 89 | empty |
| 3 | 574 | 0.74 | 0.81 | 60 | NAD, AES |
| 4 | 526 | 0.74 | 0.82 | 55 | NAD, AES |
| 5 | 61 | 0.44 | 0.82 | 11 | empty |
Interfaces
6 interfaces between chains.
- Q–R · 2044 Ų buried · 29 hydrogen bonds · protein-protein
- O–P · 2017 Ų buried · 35 hydrogen bonds · protein-protein
- O–R · 1382 Ų buried · 17 hydrogen bonds · protein-protein
- P–Q · 1354 Ų buried · 16 hydrogen bonds · protein-protein
- P–R · 557 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2B4T · Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum… · the same entry in another collection · chain O against O, 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 Q8T6B1
- Elsewhere: RCSB PDB 2B4T · PDBe 2B4T · UniProt Q8T6B1
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