MolNFT v1 · #127643 · protein
Structure of unbound briakinumab Fab
5N2K · Briakinumab Fab light chain: “Structure of unbound briakinumab Fab”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #127643 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5N2K
- Type
- protein
- Length
- 3,382 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Briakinumab Fab light chain; Briakinumab Fab heavy chain
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 14 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Briakinumab Fab light chain | protein | 216 | 6% helix, 49% strand | — |
| B | Briakinumab Fab heavy chain | protein | 212 | 8% helix, 51% strand | — |
| C | Briakinumab Fab light chain | protein | 215 | 7% helix, 50% strand | — |
| D | Briakinumab Fab heavy chain | protein | 223 | 7% helix, 49% strand | — |
| E, I | Briakinumab Fab light chain | protein | 214 | 7% helix, 50% strand | — |
| F | Briakinumab Fab heavy chain | protein | 210 | 8% helix, 52% strand | — |
| G | Briakinumab Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| H | Briakinumab Fab heavy chain | protein | 193 | 5% helix, 51% strand | — |
| J | Briakinumab Fab heavy chain | protein | 211 | 7% helix, 52% strand | — |
| K | Briakinumab Fab light chain | protein | 214 | 7% helix, 50% strand | — |
| L, N | Briakinumab Fab heavy chain | protein | 209 | 7% helix, 51% strand | — |
| M | Briakinumab Fab light chain | protein | 212 | 7% helix, 50% strand | — |
| P | Briakinumab Fab heavy chain | protein | 207 | 6% helix, 52% strand | — |
| O | Briakinumab Fab light chain | protein | 210 | 6% helix, 50% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.81 | 0.85 | 83 | empty |
| 2 | 958 | 0.74 | 0.77 | 106 | empty |
| 3 | 1080 | 0.72 | 0.76 | 105 | empty |
| 4 | 825 | 0.68 | 0.75 | 97 | empty |
| 5 | 485 | 0.64 | 0.77 | 53 | empty |
Interfaces
30 interfaces between chains.
- C–D · 1711 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1697 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1681 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1650 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1630 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 5N2K · Structure of unbound Briakinumab FAb · 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 5N2K · PDBe 5N2K
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