Research workbench
Crystal structure of human anti-steroid Fab 5F2 in complex with testosterone
Analyse Crystal structure of human anti-steroid Fab 5F2 in complex with testosterone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KDM
- Type
- protein
- Length
- 878 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin light chain; Immunoglobulin heavy chain
- Ligands
- TES
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Immunoglobulin light chain | protein | 216 | 6% helix, 49% strand | — |
| H, B | Immunoglobulin heavy chain | protein | 223 | 9% helix, 49% strand | — |
Ligands and binding sites
- TES · Testosterone · ligand · 2 copies · chains L, H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.69 | 0.75 | 95 | empty |
| 2 | 150 | 0.66 | 0.87 | 22 | TES |
| 3 | 126 | 0.65 | 0.88 | 18 | TES |
| 4 | 450 | 0.58 | 0.74 | 48 | empty |
| 5 | 52 | 0.53 | 0.89 | 19 | empty |
Interfaces
5 interfaces between chains.
- L–H · 1941 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1891 Ų buried · 14 hydrogen bonds · protein-protein
- H–B · 432 Ų buried · 16 hydrogen bonds · protein-protein
- H–A · 45 Ų buried · 1 hydrogen bond · protein-protein
- L–B · 42 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 3KDM · Crystal Structure of Human Anti-steroid Fab 5F2 in Complex with Testosterone · the same entry in another collection · chain L against L, 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 3KDM · PDBe 3KDM
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