MolNFT v1 · #61769 · protein
Crystal structure of K63-specific Fab APU.3A8 bound to K63-linked di- ubiquitin
3DVG · Human IGG1 Fab fragment light chain: “Crystal structure of K63-specific Fab APU.3A8 bound to K63-linked di- ubiquitin”. X-ray diffraction, 8 pockets (best druggability 0.61). MolNFT v1 #61769 on GenesisL1: 3D structure, binding…
- PDB
- 3DVG
- Type
- protein
- Length
- 582 residues
- Chains
- 4
- 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
- 8 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human IGG1 Fab fragment light chain | protein | 210 | 6% helix, 50% strand | — |
| B | Human IGG1 Fab fragment heavy chain | protein | 221 | 10% helix, 52% strand | — |
| X | Ubiquitin D77 | protein | 75 | 24% helix, 37% strand | P62988 |
| Y | Ubiquitin | protein | 76 | 20% helix, 32% strand | P62988 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.61 | 0.75 | 53 | empty |
| 2 | 66 | 0.55 | 0.88 | 24 | empty |
| 3 | 217 | 0.49 | 0.75 | 26 | empty |
| 4 | 174 | 0.47 | 0.76 | 26 | empty |
| 5 | 127 | 0.40 | 0.75 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2171 Ų buried · 18 hydrogen bonds · protein-protein
- B–Y · 713 Ų buried · 6 hydrogen bonds · protein-protein
- A–X · 357 Ų buried · 6 hydrogen bonds · protein-protein
- X–Y · 305 Ų buried · 5 hydrogen bonds · protein-protein
- B–X · 249 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 isopeptide (disulfide, isopeptide).
Compared structures
- 3DVG · Crystal structure of K63-specific fab Apu.3A8 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 3DVG · PDBe 3DVG · UniProt P62988
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