MolNFT v1 · #70216 · protein
Crystal structure of human STAM1 vhs domain in complex with ubiquitin
3LDZ: “Crystal structure of human STAM1 vhs domain in complex with ubiquitin”. X-ray diffraction, 8 pockets (best druggability 0.81). MolNFT v1 #70216 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3LDZ
- Type
- protein
- Length
- 779 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Signal transducing adapter molecule 1
- UniProt
- P62988, Q92783
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, E, G | Ubiquitin | protein | 73 | 25% helix, 34% strand | P62988 |
| A, D, B, C | Signal transducing adapter molecule 1 | protein | 140 | 71% helix, 0% strand | Q92783 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.81 | 0.88 | 66 | empty |
| 2 | 302 | 0.77 | 0.89 | 40 | empty |
| 3 | 278 | 0.70 | 0.85 | 39 | empty |
| 4 | 136 | 0.41 | 0.75 | 22 | empty |
| 5 | 62 | 0.36 | 0.78 | 18 | empty |
Interfaces
9 interfaces between chains.
- A–C · 661 Ų buried · 7 hydrogen bonds · protein-protein
- D–B · 578 Ų buried · 4 hydrogen bonds · protein-protein
- F–C · 447 Ų buried · 6 hydrogen bonds · protein-protein
- D–G · 408 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 404 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3LDZ · Crystal structure of human STAM1 VHS domain in complex with ubiquitin · the same entry in another collection · chain G against G, TM-score 1.00
- Q92783 · AlphaFold monomer V2.0 prediction for signal transducing adapter molecule 1 (Q92783) · a predicted model of the same protein · chain A 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 P62988
- Every structure of UniProt Q92783
- Elsewhere: RCSB PDB 3LDZ · PDBe 3LDZ · UniProt P62988 · UniProt Q92783
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