MolNFT v1 · #61776 · protein
Crystal structure of K63-specific Fab APU2.16 bound to K63-linked di- ubiquitin
3DVN · Human IGG1 Fab fragment light chain: “Crystal structure of K63-specific Fab APU2.16 bound to K63-linked di- ubiquitin”. X-ray diffraction, 17 pockets (best druggability 0.80). MolNFT v1 #61776 on GenesisL1: 3D structure, binding…
- PDB
- 3DVN
- Type
- protein
- Length
- 1,160 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human IGG1 Fab fragment light chain; Human IGG1 Fab fragment heavy chain; Ubiquitin D77…
- UniProt
- P62988
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Human IGG1 Fab fragment light chain | protein | 212 | 5% helix, 50% strand | — |
| B, H | Human IGG1 Fab fragment heavy chain | protein | 217 | 7% helix, 53% strand | — |
| X, U | Ubiquitin D77 | protein | 75 | 20% helix, 37% strand | P62988 |
| Y, V | Ubiquitin | protein | 76 | 20% helix, 33% strand | P62988 |
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.80 | 0.82 | 128 | empty |
| 2 | 313 | 0.69 | 0.84 | 56 | empty |
| 3 | 326 | 0.66 | 0.81 | 49 | empty |
| 4 | 177 | 0.58 | 0.81 | 29 | empty |
| 5 | 220 | 0.48 | 0.75 | 32 | empty |
Interfaces
15 interfaces between chains.
- L–H · 2083 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2007 Ų buried · 15 hydrogen bonds · protein-protein
- A–L · 1433 Ų buried · 23 hydrogen bonds · protein-protein
- B–Y · 717 Ų buried · 7 hydrogen bonds · protein-protein
- H–V · 706 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 isopeptide (disulfide, isopeptide).
Compared structures
- 3DVN · Crystal structure of K63-specific fab Apu2.16 bound to K63-linked di-ubiquitin · the same entry in another collection · chain A against A, 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 P62988
- Elsewhere: RCSB PDB 3DVN · PDBe 3DVN · UniProt P62988
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.