MolNFT v1 · #23703 · protein
Crystal structure of human placental glyceraldehyde-3- phosphate dehydrogenase at 1.75 resolution
1U8F · Glyceraldehyde-3-phosphate dehydrogenase, liver: “Crystal structure of human placental glyceraldehyde-3- phosphate dehydrogenase at 1.75 resolution”. X-ray diffraction, 1 ligand (NAD), 9 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 1U8F
- 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, liver
- EC
- 1.2.1.12
- UniProt
- P04406
- Ligands
- NAD
- Pockets
- 9 · best druggability 0.77
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, liver (EC 1.2.1.12) | protein | 333 | 30% helix, 27% strand | P04406 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains P, Q, O, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.77 | 0.79 | 113 | NAD |
| 2 | 461 | 0.76 | 0.85 | 45 | empty |
| 3 | 948 | 0.76 | 0.79 | 124 | NAD |
| 4 | 584 | 0.73 | 0.81 | 68 | empty |
| 5 | 77 | 0.36 | 0.76 | 14 | empty |
Interfaces
6 interfaces between chains.
- Q–R · 2032 Ų buried · 36 hydrogen bonds · protein-protein
- O–P · 1999 Ų buried · 34 hydrogen bonds · protein-protein
- P–Q · 1438 Ų buried · 25 hydrogen bonds · protein-protein
- O–R · 1435 Ų buried · 25 hydrogen bonds · protein-protein
- P–R · 557 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1U8F · Crystal Structure Of Human Placental Glyceraldehyde-3-Phosphate Dehydrogenase At 1.75… · the same entry in another collection · chain P against P, TM-score 1.00
- P04406 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P04406) · a predicted model of the same protein · chain P 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 1U8F · PDBe 1U8F · UniProt P04406
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