MolNFT v2 · #216297 · protein
Human wild-type GAPDH,orthorhombic form
8P5F · Glyceraldehyde-3-phosphate dehydrogenase: “Human wild-type GAPDH,orthorhombic form”. X-ray diffraction at 1.82, 2 ligands (NAD, ZN), 8 pockets (best druggability 0.77). MolNFT v2 #216297 on GenesisL1: 3D structure, binding sites and…
- PDB
- 8P5F
- Type
- protein
- Length
- 1,333 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.82
- Source
- Homo sapiens
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12, 2.6.99.-
- UniProt
- P04406
- Ligands
- NAD, ZN
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.82 · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-) | protein | 334 | 32% helix, 27% strand | P04406 |
| DDD, EEE, GGG | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12, 2.6.99.-) | protein | 333 | 32% helix, 27% strand | P04406 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains AAA, GGG, DDD, EEE
- ZN · Zinc ion · metal · 2 copies · chains EEE
- ACT · Acetate ion · additive · chains EEE
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.77 | 0.82 | 71 | empty |
| 2 | 574 | 0.76 | 0.83 | 63 | empty |
| 3 | 702 | 0.71 | 0.78 | 81 | NAD |
| 4 | 648 | 0.68 | 0.77 | 69 | NAD |
| 5 | 531 | 0.68 | 0.78 | 72 | NAD |
Interfaces
6 interfaces between chains.
- DDD–GGG · 1997 Ų buried · 33 hydrogen bonds · protein-protein
- AAA–EEE · 1995 Ų buried · 33 hydrogen bonds · protein-protein
- DDD–EEE · 1443 Ų buried · 24 hydrogen bonds · protein-protein
- AAA–GGG · 1440 Ų buried · 26 hydrogen bonds · protein-protein
- EEE–GGG · 458 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- P04406 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P04406) · a predicted model of the same protein · chain DDD 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 P04406
- Elsewhere: RCSB PDB 8P5F · PDBe 8P5F · UniProt P04406
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