MolNFT v1 · #168512 · protein
Crystal structure of nhp D15.SD7 Fab in complex with 16055 V1V2 1FD6 scaffold
6WIT · Nhp GN1-SD7 Fab heavy chain: “Crystal structure of nhp D15.SD7 Fab in complex with 16055 V1V2 1FD6 scaffold”. X-ray diffraction, 2 ligands (NAG, SO4), 17 pockets (best druggability 0.81). MolNFT v1 #168512 on GenesisL1: 3D…
- 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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