MolNFT v1 · #53514 · protein
Crystal structure of methylmalonic acidemia type a protein
2WWW · Methylmalonic aciduria type a protein, mitochondrial: “Crystal structure of methylmalonic acidemia type a protein”. X-ray diffraction, 1 ligand (GDP), 15 pockets (best druggability 0.66). MolNFT v1 #53514 on GenesisL1: 3D structure…
- PDB
- 2WWW
- Type
- protein
- Length
- 1,203 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylmalonic aciduria type a protein, mitochondrial
- UniProt
- Q8IVH4
- Ligands
- GDP
- Pockets
- 15 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylmalonic aciduria type a protein, mitochondrial | protein | 298 | 57% helix, 11% strand | Q8IVH4 |
| B | Methylmalonic aciduria type a protein, mitochondrial | protein | 299 | 56% helix, 11% strand | Q8IVH4 |
| C | Methylmalonic aciduria type a protein, mitochondrial | protein | 292 | 59% helix, 11% strand | Q8IVH4 |
| D | Methylmalonic aciduria type a protein, mitochondrial | protein | 314 | 56% helix, 11% strand | Q8IVH4 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- 2PE · Nonaethylene glycol · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.66 | 0.78 | 64 | empty |
| 2 | 208 | 0.65 | 0.84 | 28 | empty |
| 3 | 387 | 0.64 | 0.79 | 45 | empty |
| 4 | 199 | 0.64 | 0.84 | 28 | empty |
| 5 | 341 | 0.63 | 0.79 | 36 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2017 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1959 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 51 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 Q8IVH4
- Elsewhere: RCSB PDB 2WWW · PDBe 2WWW · UniProt Q8IVH4
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