Research workbench
Structural and biochemical basis for the inhibition of cell death by apip, a methionine salvage enzyme
Analyse Structural and biochemical basis for the inhibition of cell death by apip, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M6R
- Type
- protein
- Length
- 893 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylthioribulose-1-phosphate dehydratase
- EC
- 4.2.1.109
- UniProt
- Q96GX9
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Methylthioribulose-1-phosphate dehydratase (EC 4.2.1.109) | protein | 224 | 40% helix, 21% strand | Q96GX9 |
| D | Methylthioribulose-1-phosphate dehydratase (EC 4.2.1.109) | protein | 221 | 40% helix, 22% strand | Q96GX9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.75 | 0.78 | 81 | empty |
| 2 | 357 | 0.66 | 0.80 | 44 | ZN |
| 3 | 386 | 0.65 | 0.79 | 49 | ZN |
| 4 | 358 | 0.64 | 0.79 | 49 | ZN |
| 5 | 353 | 0.63 | 0.79 | 39 | ZN |
Interfaces
4 interfaces between chains.
- B–C · 1514 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1511 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1504 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1135 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4M6R · Structural and biochemical basis for the inhibition of cell death by APIP, a methionine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96GX9 · AlphaFold monomer V2.0 prediction for methylthioribulose-1-phosphate dehydratase (Q96GX9) · a predicted model of the same protein · 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 Q96GX9
- Elsewhere: RCSB PDB 4M6R · PDBe 4M6R · UniProt Q96GX9
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