Research workbench
Crystal structure of clfa in complex with the Fab fragment of tefibazumab
Analyse Crystal structure of clfa in complex with the Fab fragment of tefibazumab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JQ6
- Type
- protein
- Length
- 736 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clumping factor a; Tefibazumab Fab fragment heavy chain; Tefibazumab Fab fragment light…
- UniProt
- G0XY13
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clumping factor a | protein | 320 | 6% helix, 49% strand | G0XY13 |
| H | Tefibazumab Fab fragment heavy chain | protein | 204 | 10% helix, 49% strand | — |
| L | Tefibazumab Fab fragment light chain | protein | 212 | 6% helix, 49% strand | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.72 | 0.91 | 26 | empty |
| 2 | 401 | 0.71 | 0.83 | 62 | empty |
| 3 | 130 | 0.38 | 0.74 | 28 | empty |
| 4 | 93 | 0.35 | 0.75 | 23 | empty |
| 5 | 64 | 0.33 | 0.76 | 12 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1575 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 594 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 532 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5JQ6 · Crystal structure of ClfA in complex with the Fab fragment of Tefibazumab · 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 G0XY13
- Elsewhere: RCSB PDB 5JQ6 · PDBe 5JQ6 · UniProt G0XY13
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.