MolNFT v1 · #126537 · protein
Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 2)
5M5V · Clathrin heavy chain 1: “Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen…”. X-ray diffraction, 5 pockets (best druggability 0.82). MolNFT v1 #126537 on GenesisL1: 3D…
- PDB
- 5M5V
- Type
- protein
- Length
- 752 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clathrin heavy chain 1; Large delta antigen
- UniProt
- P49951, A4ZNG7
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Clathrin heavy chain 1 | protein | 360 | 9% helix, 51% strand | P49951 |
| E, F | Large delta antigen | protein | 6 | 0% helix, 17% strand | A4ZNG7 |
| G, H | Large delta antigen | protein | 6 | 0% helix, 0% strand | A4ZNG7 |
| I, J | Large delta antigen | protein | 4 | 0% helix, 0% strand | A4ZNG7 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.82 | 0.83 | 117 | empty |
| 2 | 639 | 0.74 | 0.81 | 67 | empty |
| 3 | 55 | 0.30 | 0.76 | 17 | empty |
| 4 | 51 | 0.28 | 0.75 | 17 | empty |
| 5 | 50 | 0.24 | 0.73 | 17 | empty |
Interfaces
8 interfaces between chains.
- A–B · 943 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 461 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 458 Ų buried · 3 hydrogen bonds · protein-protein
- B–H · 412 Ų buried · 6 hydrogen bonds · protein-protein
- A–G · 403 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5M5V · Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D… · the same entry in another collection · chain J against J, TM-score 1.00
- P49951 · AlphaFold monomer V2.0 prediction for clathrin heavy chain 1 (P49951) · 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 P49951
- Every structure of UniProt A4ZNG7
- Elsewhere: RCSB PDB 5M5V · PDBe 5M5V · UniProt P49951 · UniProt A4ZNG7
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