Research workbench
Chicken scap D435V L1-L7 domain / Fab complex focused MAP
Analyse Chicken scap D435V L1-L7 domain / Fab complex focused MAP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LKH
- Type
- protein
- Length
- 516 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sterol regulatory element-binding protein cleavage- activating protein; 4G10 Fab heavy…
- UniProt
- A0A3Q3ANV4
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.58
Structure
electron microscopy · 3 distinct chains · 19% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sterol regulatory element-binding protein cleavage- activating protein | protein | 286 | 29% helix, 17% strand | A0A3Q3ANV4 |
| H | 4G10 Fab heavy chain | protein | 121 | 7% helix, 47% strand | — |
| L | 4G10 Fab kappa chain | protein | 109 | 3% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.58 | 0.75 | 47 | empty |
| 2 | 96 | 0.41 | 0.77 | 15 | empty |
| 3 | 80 | 0.38 | 0.77 | 17 | empty |
| 4 | 80 | 0.36 | 0.76 | 25 | empty |
| 5 | 55 | 0.28 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 866 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 621 Ų buried · 16 hydrogen bonds · protein-protein
- A–L · 350 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7LKH · Chicken Scap D435V L1-L7 domain / Fab complex focused map · 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
- Every structure of UniProt A0A3Q3ANV4
- Elsewhere: RCSB PDB 7LKH · PDBe 7LKH · UniProt A0A3Q3ANV4
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