MolNFT v1 · #107034 · protein
Crystal structure of LIP5 N-terminal domain complexed with CHMP1B mim and CHMP5 mim
4TXR · Charged multivesicular body protein 1B: “Crystal structure of LIP5 N-terminal domain complexed with CHMP1B mim and CHMP5 mim”. X-ray diffraction, 2 pockets (best druggability 0.42). MolNFT v1 #107034 on GenesisL1: 3D structure…
- PDB
- 4TXR
- Type
- protein
- Length
- 214 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Charged multivesicular body protein 1B; Vacuolar protein sorting-associated protein VTA1…
- UniProt
- Q7LBR1, Q9NP79, Q9NZZ3
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Charged multivesicular body protein 1B | protein | 15 | 67% helix, 0% strand | Q7LBR1 |
| A | Vacuolar protein sorting-associated protein VTA1 homolog | protein | 159 | 78% helix, 0% strand | Q9NP79 |
| C | Charged multivesicular body protein 5 | protein | 40 | 58% helix, 0% strand | Q9NZZ3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.42 | 0.78 | 16 | empty |
| 2 | 70 | 0.35 | 0.76 | 14 | EDO |
Interfaces
2 interfaces between chains.
- A–C · 1529 Ų buried · 20 hydrogen bonds · protein-protein
- B–A · 673 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4TXR · Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM and CHMP5 MIM · the same entry in another collection · chain B against B, TM-score 1.00
- Q9NP79 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein VTA1… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q7LBR1 · AlphaFold monomer V2.0 prediction for charged multivesicular body protein 1B (Q7LBR1) · a predicted model of the same protein · chain B against A, TM-score 0.68
- Q9NZZ3 · AlphaFold monomer V2.0 prediction for charged multivesicular body protein 5 (Q9NZZ3) · a predicted model of the same protein · chain C against A, TM-score 0.49
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 Q7LBR1
- Every structure of UniProt Q9NP79
- Every structure of UniProt Q9NZZ3
- Elsewhere: RCSB PDB 4TXR · PDBe 4TXR · UniProt Q7LBR1 · UniProt Q9NP79 · UniProt Q9NZZ3
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