Research workbench
Monoclinic crystal form of the extracellular olfactomedin domain from gliomedin
Analyse Monoclinic crystal form of the extracellular olfactomedin domain from gliomedin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D7C
- Type
- protein
- Length
- 491 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gliomedin
- UniProt
- Q80WL1
- Ligands
- NA
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gliomedin | protein | 246 | 4% helix, 54% strand | Q80WL1 |
| B | Gliomedin | protein | 245 | 4% helix, 56% strand | Q80WL1 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.57 | 0.82 | 25 | empty |
| 2 | 121 | 0.42 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 471 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4D7C · Monoclinic crystal form of the extracellular olfactomedin domain from gliomedin · the same entry in another collection · chain A against A, TM-score 1.00
- Q80WL1 · AlphaFold monomer V2.0 prediction for gliomedin (Q80WL1) · a predicted model of the same protein · chain B 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 Q80WL1
- Elsewhere: RCSB PDB 4D7C · PDBe 4D7C · UniProt Q80WL1
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