MolNFT v1 · #18351 · protein
Crystal structure of yersinia pseudotuberculosis-derived mitogen (ypm)
1PM4: “Crystal structure of yersinia pseudotuberculosis-derived mitogen (ypm)”. X-ray diffraction, 4 pockets (best druggability 0.76). MolNFT v1 #18351 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1PM4
- Type
- protein
- Length
- 351 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ypm
- UniProt
- Q57221
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ypm | protein | 117 | 3% helix, 53% strand | Q57221 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.76 | 0.82 | 60 | empty |
| 2 | 50 | 0.46 | 0.85 | 14 | empty |
| 3 | 72 | 0.43 | 0.81 | 18 | empty |
| 4 | 76 | 0.29 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 533 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 517 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 506 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1PM4 · Crystal structure of Yersinia pseudotuberculosis-derived mitogen (YPM) · the same entry in another collection · 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 Q57221
- Elsewhere: RCSB PDB 1PM4 · PDBe 1PM4 · UniProt Q57221
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