Research workbench
Crystal structure of nhp D15.SD7 Fab in complex with 16055 V1V2 1FD6 scaffold
Analyse Crystal structure of nhp D15.SD7 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
- 6WIT
- Type
- protein
- Length
- 1,061 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nhp GN1-SD7 Fab heavy chain; Nhp GN1-SD7 Fab light chain; 16055 V1V2 1FD6 scaffold
- Ligands
- NAG, SO4
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nhp GN1-SD7 Fab heavy chain | protein | 226 | 7% helix, 54% strand | — |
| B | Nhp GN1-SD7 Fab light chain | protein | 210 | 5% helix, 50% strand | — |
| C | 16055 V1V2 1FD6 scaffold | protein | 102 | 17% helix, 49% strand | — |
| H | Nhp GN1-SD7 Fab heavy chain | protein | 223 | 7% helix, 54% strand | — |
| L | Nhp GN1-SD7 Fab light chain | protein | 213 | 6% helix, 50% strand | — |
| I | 16055 V1V2 1FD6 scaffold | protein | 87 | 14% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, I, L
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.81 | 0.83 | 107 | SO4 |
| 2 | 866 | 0.77 | 0.80 | 97 | SO4 |
| 3 | 65 | 0.68 | 0.95 | 20 | empty |
| 4 | 317 | 0.62 | 0.79 | 33 | empty |
| 5 | 487 | 0.59 | 0.74 | 56 | SO4 |
Interfaces
9 interfaces between chains.
- A–B · 1882 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 1790 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 665 Ų buried · 5 hydrogen bonds · protein-protein
- C–H · 590 Ų buried · 15 hydrogen bonds · protein-protein
- A–I · 590 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6WIT · Crystal structure of NHP D15.SD7 Fab in complex with 16055 V1V2 1FD6 scaffold · 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
- Elsewhere: RCSB PDB 6WIT · PDBe 6WIT
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