MolNFT v1 · #86898 · protein
Crystal structure of the arthritogenic antibody M2139 (Fab fragment) in complex with the triple-helical J1 peptide
4BKL · M2139 Fab fragment heavy chain: “Crystal structure of the arthritogenic antibody M2139 (Fab fragment) in complex with the triple-helical J1…”. X-ray diffraction, 6 pockets (best druggability 0.57). MolNFT v1 #86898 on GenesisL1: 3D…
- PDB
- 4BKL
- Type
- protein
- Length
- 508 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M2139 Fab fragment heavy chain; M2139 Fab fragment light chain; J1 epitope
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M2139 Fab fragment heavy chain | protein | 216 | 3% helix, 53% strand | — |
| B | M2139 Fab fragment light chain | protein | 216 | 7% helix, 56% strand | — |
| E | J1 epitope | protein | 25 | 0% helix, 0% strand | — |
| F | J1 epitope | protein | 26 | 0% helix, 0% strand | — |
| G | J1 epitope | protein | 25 | 0% helix, 4% strand | — |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.57 | 0.74 | 57 | empty |
| 2 | 119 | 0.42 | 0.76 | 22 | empty |
| 3 | 114 | 0.38 | 0.74 | 23 | empty |
| 4 | 100 | 0.37 | 0.74 | 20 | empty |
| 5 | 76 | 0.33 | 0.75 | 21 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1733 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 839 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 828 Ų buried · 14 hydrogen bonds · protein-protein
- E–G · 787 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 378 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified, 4 disulfide (hydroxylation, disulfide).
Compared structures
- 4BKL · Crystal structure of the arthritogenic antibody M2139 (Fab fragment) in complex with the… · 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
- Elsewhere: RCSB PDB 4BKL · PDBe 4BKL
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