Research workbench
Crystal structure of nhp VD20.5A4 Fab in complex with 16055 V1V2 1FD6 scaffold
Analyse Crystal structure of nhp VD20.5A4 Fab in complex with 16055 V1V2 1FD6 scaffold in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XSN
- Type
- protein
- Length
- 476 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VD20.5A4_HEAVY_CHAIN; VD20.5A4_LIGHT_CHAIN; 16055_V1V2-1FD6
- Ligands
- NAG, NA, SCN
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | VD20.5A4_HEAVY_CHAIN | protein | 214 | 8% helix, 55% strand | — |
| L | VD20.5A4_LIGHT_CHAIN | protein | 214 | 6% helix, 50% strand | — |
| C | 16055_V1V2-1FD6 | protein | 48 | 0% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- NA · Sodium ion · metal · chains H, L, C
- SCN · Thiocyanate ion · ion · 3 copies · chains H, L
- EDO · 1,2-ethanediol · additive · 4 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.60 | 0.74 | 51 | SCN, EDO |
| 2 | 58 | 0.34 | 0.78 | 22 | empty |
| 3 | 68 | 0.31 | 0.74 | 17 | empty |
| 4 | 76 | 0.29 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1727 Ų buried · 14 hydrogen bonds · protein-protein
- H–C · 459 Ų buried · 7 hydrogen bonds · protein-protein
- L–C · 191 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6XSN · Crystal structure of NHP VD20.5A4 Fab in complex with 16055 V1V2 1FD6 scaffold · the same entry in another collection · chain H against H, 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 6XSN · PDBe 6XSN
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