MolNFT v1 · #82385 · protein
Crystal structure of edgp
3VLA: “Crystal structure of edgp”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.58). MolNFT v1 #82385 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VLA
- Type
- protein
- Length
- 413 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Edgp
- UniProt
- Q05929
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Edgp | protein | 413 | 13% helix, 40% strand | Q05929 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.58 | 0.80 | 39 | empty |
| 2 | 101 | 0.42 | 0.78 | 20 | empty |
| 3 | 52 | 0.36 | 0.79 | 13 | empty |
| 4 | 62 | 0.28 | 0.74 | 19 | empty |
| 5 | 62 | 0.25 | 0.72 | 18 | empty |
Modifications
Observed in the structure: 6 disulfide, 4 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 3VLA · Crystal structure of edgp · 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 Q05929
- Elsewhere: RCSB PDB 3VLA · PDBe 3VLA · UniProt Q05929
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