Research workbench
Acropora millepora GAPDH
Analyse Acropora millepora GAPDH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PX2
- Type
- protein
- Length
- 2,656 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- A0A3F2YLZ0
- Ligands
- NAD, PO4
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 332 | 30% helix, 27% strand | A0A3F2YLZ0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, D, B, C, E, H, F, G
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.82 | 0.83 | 111 | empty |
| 2 | 1178 | 0.80 | 0.82 | 117 | empty |
| 3 | 1085 | 0.77 | 0.79 | 121 | NAD, PO4 |
| 4 | 1197 | 0.76 | 0.78 | 114 | NAD, PO4 |
| 5 | 478 | 0.70 | 0.81 | 58 | NAD, PO4 |
Interfaces
14 interfaces between chains.
- A–B · 2021 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 1984 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1983 Ų buried · 32 hydrogen bonds · protein-protein
- G–H · 1970 Ų buried · 31 hydrogen bonds · protein-protein
- E–H · 1437 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6PX2 · Acropora millepora GAPDH · 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 A0A3F2YLZ0
- Elsewhere: RCSB PDB 6PX2 · PDBe 6PX2 · UniProt A0A3F2YLZ0
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