MolNFT v1 · #92994 · protein
The structure of lobster apo-D-glyceraldehyde-3-phosphate dehydrogenase at 3.0 ångströms resolution
4GPD: “The structure of lobster apo-D-glyceraldehyde-3-phosphate dehydrogenase at 3.0 ångströms resolution”. X-ray diffraction, 9 pockets (best druggability 0.80). MolNFT v1 #92994 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4GPD
- Type
- protein
- Length
- 1,332 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apo-D-glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- P00357
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2, 3, 4 | Apo-D-glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 333 | 29% helix, 21% strand | P00357 |
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 | 949 | 0.80 | 0.82 | 119 | empty |
| 2 | 1135 | 0.75 | 0.78 | 127 | empty |
| 3 | 733 | 0.70 | 0.76 | 77 | empty |
| 4 | 609 | 0.68 | 0.77 | 70 | empty |
| 5 | 115 | 0.37 | 0.74 | 21 | empty |
Interfaces
6 interfaces between chains.
- 1–4 · 1905 Ų buried · 32 hydrogen bonds · protein-protein
- 2–3 · 1865 Ų buried · 26 hydrogen bonds · protein-protein
- 1–2 · 1266 Ų buried · 20 hydrogen bonds · protein-protein
- 3–4 · 1257 Ų buried · 23 hydrogen bonds · protein-protein
- 1–3 · 431 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4GPD · The structure of lobster apo-D-glyceraldehyde-3-phosphate dehydrogenase at 3.0 ångströms… · the same entry in another collection · chain 4 against 4, TM-score 1.00
- P00357 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase (P00357) · a predicted model of the same protein · chain 2 against A, TM-score 0.98
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 P00357
- Elsewhere: RCSB PDB 4GPD · PDBe 4GPD · UniProt P00357
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