Research workbench
Structure of nhp D11A.B5FAB in complex with 16055 V2B peptide
Analyse Structure of nhp D11A.B5FAB in complex with 16055 V2B peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VJN
- Type
- protein
- Length
- 455 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D11A.B5 Fab heavy chain; D11A.B5 Fab light chain; V2B peptide
- Ligands
- NA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | D11A.B5 Fab heavy chain | protein | 214 | 7% helix, 55% strand | — |
| L | D11A.B5 Fab light chain | protein | 212 | 8% helix, 49% strand | — |
| G | V2B peptide | protein | 19 | 0% helix, 42% strand | — |
| F | V2B peptide | protein | 10 | 0% helix, 40% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains H, L, G, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 87 | 0.74 | 0.96 | 19 | empty |
| 2 | 478 | 0.57 | 0.73 | 47 | empty |
| 3 | 75 | 0.39 | 0.78 | 17 | empty |
| 4 | 87 | 0.38 | 0.77 | 22 | NA |
| 5 | 79 | 0.30 | 0.73 | 19 | empty |
Interfaces
6 interfaces between chains.
- H–L · 1522 Ų buried · 15 hydrogen bonds · protein-protein
- G–F · 545 Ų buried · 10 hydrogen bonds · protein-protein
- H–G · 415 Ų buried · 5 hydrogen bonds · protein-protein
- L–G · 360 Ų buried · 5 hydrogen bonds · protein-protein
- H–F · 198 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6VJN · Structure of NHP D11A.B5Fab in complex with 16055 V2b peptide · 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 6VJN · PDBe 6VJN
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