MolNFT v1 · #56663 · protein
Integrated structural and functional model of the human escrt-II complex
2ZME · Vacuolar-sorting protein SNF8: “Integrated structural and functional model of the human escrt-II complex”. X-ray diffraction, 7 pockets (best druggability 0.76). MolNFT v1 #56663 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2ZME
- Type
- protein
- Length
- 628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar-sorting protein SNF8; Vacuolar protein-sorting-associated protein 36; Vacuolar…
- UniProt
- Q96H20, Q86VN1, Q9BRG1
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar-sorting protein SNF8 | protein | 217 | 56% helix, 10% strand | Q96H20 |
| B | Vacuolar protein-sorting-associated protein 36 | protein | 215 | 55% helix, 12% strand | Q86VN1 |
| C | Vacuolar protein-sorting-associated protein 25 | protein | 99 | 48% helix, 14% strand | Q9BRG1 |
| D | Vacuolar protein-sorting-associated protein 25 | protein | 97 | 45% helix, 10% strand | Q9BRG1 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.76 | 0.78 | 117 | empty |
| 2 | 58 | 0.60 | 0.90 | 18 | empty |
| 3 | 159 | 0.52 | 0.79 | 30 | empty |
| 4 | 221 | 0.52 | 0.76 | 34 | empty |
| 5 | 50 | 0.30 | 0.76 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2341 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 891 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 769 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 286 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2ZME · Integrated structural and functional model of the human ESCRT-II complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BRG1 · AlphaFold monomer V2.0 prediction for vacuolar protein-sorting- associated protein 25… · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q96H20 · AlphaFold monomer V2.0 prediction for vacuolar-sorting protein SNF8 (Q96H20) · a predicted model of the same protein · chain A against A, TM-score 0.89
- Q86VN1 · AlphaFold monomer V2.0 prediction for vacuolar protein-sorting- associated protein 36… · a predicted model of the same protein · chain B against A, TM-score 0.72
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 Q96H20
- Every structure of UniProt Q86VN1
- Every structure of UniProt Q9BRG1
- Elsewhere: RCSB PDB 2ZME · PDBe 2ZME · UniProt Q96H20 · UniProt Q86VN1 · UniProt Q9BRG1
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