Research workbench
Tnfalpha-certolizumab Fab
Analyse Tnfalpha-certolizumab Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WUX
- Type
- protein
- Length
- 1,668 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy; Light; Tumor necrosis factor alpha
- UniProt
- C1K3N5
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heavy | protein | 210 | 4% helix, 51% strand | — |
| B | Light | protein | 212 | 6% helix, 50% strand | — |
| C | Heavy | protein | 202 | 3% helix, 49% strand | — |
| D | Light | protein | 201 | 3% helix, 46% strand | — |
| H | Heavy | protein | 212 | 6% helix, 52% strand | — |
| L | Light | protein | 213 | 6% helix, 51% strand | — |
| E | Tumor necrosis factor alpha | protein | 136 | 2% helix, 51% strand | C1K3N5 |
| F, G | Tumor necrosis factor alpha | protein | 141 | 2% helix, 53% strand | C1K3N5 |
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.76 | 0.99 | 18 | empty |
| 2 | 559 | 0.71 | 0.80 | 78 | empty |
| 3 | 504 | 0.71 | 0.80 | 73 | empty |
| 4 | 448 | 0.71 | 0.81 | 48 | empty |
| 5 | 360 | 0.71 | 0.83 | 40 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1749 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1747 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1721 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 1143 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1059 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 5WUX · TNFalpha-certolizumab 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
- Every structure of UniProt C1K3N5
- Elsewhere: RCSB PDB 5WUX · PDBe 5WUX · UniProt C1K3N5
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