Research workbench
Crystal structure of a human ependymin related protein
Analyse Crystal structure of a human ependymin related protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JLD
- Type
- protein
- Length
- 732 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mammalian ependymin-related protein 1
- UniProt
- Q9UM22
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mammalian ependymin-related protein 1 | protein | 185 | 5% helix, 48% strand | Q9UM22 |
| B | Mammalian ependymin-related protein 1 | protein | 183 | 7% helix, 49% strand | Q9UM22 |
| C | Mammalian ependymin-related protein 1 | protein | 184 | 6% helix, 50% strand | Q9UM22 |
| D | Mammalian ependymin-related protein 1 | protein | 180 | 7% helix, 49% strand | Q9UM22 |
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.88 | 0.89 | 127 | empty |
| 2 | 870 | 0.79 | 0.82 | 73 | empty |
| 3 | 827 | 0.75 | 0.79 | 55 | empty |
| 4 | 65 | 0.74 | 0.98 | 17 | empty |
| 5 | 71 | 0.71 | 0.96 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2020 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1929 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 474 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 381 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 104 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6JLD · Crystal structure of a human ependymin related protein · the same entry in another collection · chain D against D, TM-score 1.00
- Q9UM22 · AlphaFold monomer V2.0 prediction for mammalian ependymin-related protein 1 (Q9UM22) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q9UM22
- Elsewhere: RCSB PDB 6JLD · PDBe 6JLD · UniProt Q9UM22
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