MolNFT v1 · #116829 · protein
Crystal structure of PLEKHM1 lir in complex with human LC3C_8-125
5DPW · Microtubule-associated proteins 1A/1B light chain 3C: “Crystal structure of PLEKHM1 lir in complex with human LC3C_8-125”. X-ray diffraction, 20 pockets (best druggability 0.67). MolNFT v1 #116829 on GenesisL1: 3D structure, binding…
- PDB
- 5DPW
- Type
- protein
- Length
- 992 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Microtubule-associated proteins 1A/1B light chain 3C; Pleckstrin homology…
- UniProt
- Q9BXW4, Q9Y4G2
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O | Microtubule-associated proteins 1A/1B light chain 3C | protein | 115 | 31% helix, 23% strand | Q9BXW4 |
| B, D, F, H, J, L, N, P | Pleckstrin homology domain-containing family M member 1 | protein | 9 | 0% helix, 33% strand | Q9Y4G2 |
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.67 | 0.79 | 47 | empty |
| 2 | 225 | 0.56 | 0.78 | 23 | empty |
| 3 | 217 | 0.53 | 0.77 | 24 | empty |
| 4 | 197 | 0.51 | 0.76 | 22 | empty |
| 5 | 182 | 0.49 | 0.77 | 27 | empty |
Interfaces
24 interfaces between chains.
- A–E · 899 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 850 Ų buried · 12 hydrogen bonds · protein-protein
- I–M · 824 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 720 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 678 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5DPW · Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 · the same entry in another collection · chain P against P, 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 Q9BXW4
- Every structure of UniProt Q9Y4G2
- Elsewhere: RCSB PDB 5DPW · PDBe 5DPW · UniProt Q9BXW4 · UniProt Q9Y4G2
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