MolNFT v1 · #153661 · protein
Crystal structure of a mouse ependymin related protein
6JLA · Mammalian ependymin-related protein 1: “Crystal structure of a mouse ependymin related protein”. X-ray diffraction, 2 ligands (NAG, FUC), 7 pockets (best druggability 0.82). MolNFT v1 #153661 on GenesisL1: 3D structure, binding…
- PDB
- 6JLA
- Type
- protein
- Length
- 738 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mammalian ependymin-related protein 1
- UniProt
- Q99M71
- Ligands
- NAG, FUC
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Mammalian ependymin-related protein 1 | protein | 184 | 4% helix, 50% strand | Q99M71 |
| B | Mammalian ependymin-related protein 1 | protein | 182 | 5% helix, 48% strand | Q99M71 |
| D | Mammalian ependymin-related protein 1 | protein | 188 | 4% helix, 48% strand | Q99M71 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, D
- FUC · alpha-L-fucopyranose · sugar · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.82 | 0.84 | 75 | empty |
| 2 | 908 | 0.81 | 0.83 | 92 | empty |
| 3 | 912 | 0.79 | 0.81 | 79 | empty |
| 4 | 119 | 0.78 | 0.97 | 26 | empty |
| 5 | 696 | 0.77 | 0.81 | 62 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2200 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 2062 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 355 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6JLA · Crystal structure of a mouse ependymin related protein · the same entry in another collection · chain C against C, TM-score 1.00
- Q99M71 · AlphaFold monomer V2.0 prediction for mammalian ependymin-related protein 1 (Q99M71) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q99M71
- Elsewhere: RCSB PDB 6JLA · PDBe 6JLA · UniProt Q99M71
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