Research workbench
Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic csim tetrapeptide from the C-terminus of prelamin a
Analyse Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YPT
- Type
- protein
- Length
- 1,683 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caax prenyl protease 1 homolog; Prelamin-A/C
- EC
- 3.4.24.84
- UniProt
- O75844, P02545
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caax prenyl protease 1 homolog (EC 3.4.24.84) | protein | 424 | 72% helix, 4% strand | O75844 |
| B | Caax prenyl protease 1 homolog (EC 3.4.24.84) | protein | 416 | 73% helix, 4% strand | O75844 |
| D | Caax prenyl protease 1 homolog (EC 3.4.24.84) | protein | 415 | 73% helix, 4% strand | O75844 |
| E | Caax prenyl protease 1 homolog (EC 3.4.24.84) | protein | 414 | 73% helix, 4% strand | O75844 |
| F, I | Prelamin-A/C | protein | 3 | 0% helix, 0% strand | P02545 |
| G, H | Prelamin-A/C | protein | 4 | 0% helix, 0% strand | P02545 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, F, B, G, D, H, E, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.72 | 0.80 | 74 | empty |
| 2 | 458 | 0.70 | 0.80 | 45 | empty |
| 3 | 270 | 0.69 | 0.84 | 40 | empty |
| 4 | 746 | 0.69 | 0.76 | 79 | empty |
| 5 | 690 | 0.69 | 0.76 | 65 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1482 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1471 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 445 Ų buried · 5 hydrogen bonds · protein-protein
- B–G · 438 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 341 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2YPT · Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant… · the same entry in another collection · chain I against I, TM-score 1.00
- O75844 · AlphaFold monomer V2.0 prediction for caax prenyl protease 1 homolog (O75844) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 O75844
- Every structure of UniProt P02545
- Elsewhere: RCSB PDB 2YPT · PDBe 2YPT · UniProt O75844 · UniProt P02545
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