MolNFT v1 · #75275 · protein
Reverse binding mode of metrd peptide complexed with C-cbl tkb domain
3PLF: “Reverse binding mode of metrd peptide complexed with C-cbl tkb domain”. X-ray diffraction, 2 ligands (CA, CL), 8 pockets (best druggability 0.74). MolNFT v1 #75275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3PLF
- Type
- protein
- Length
- 610 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metrd peptide; E3 ubiquitin-protein ligase cbl
- EC
- 6.3.2.-
- UniProt
- P22681
- Ligands
- CA, CL
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Metrd peptide | protein | 4 | 0% helix, 0% strand | — |
| B, D | E3 ubiquitin-protein ligase cbl (EC 6.3.2.-) | protein | 301 | 57% helix, 8% strand | P22681 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.74 | 0.86 | 45 | CL |
| 2 | 465 | 0.73 | 0.83 | 58 | CL |
| 3 | 150 | 0.66 | 0.88 | 20 | empty |
| 4 | 130 | 0.55 | 0.82 | 19 | empty |
| 5 | 109 | 0.53 | 0.83 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–D · 816 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 388 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 383 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3PLF · Reverse Binding Mode of MetRD peptide complexed with c-Cbl TKB domain · the same entry in another collection · chain D against D, TM-score 1.00
- P22681 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase cbl (P22681) · a predicted model of the same protein · chain B 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 P22681
- Elsewhere: RCSB PDB 3PLF · PDBe 3PLF · UniProt P22681
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