Research workbench
Crystal structure of the self-assembled propeptides from APE1
Analyse Crystal structure of the self-assembled propeptides from APE1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JHC
- Type
- protein
- Length
- 914 residues
- Chains
- 39
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar aminopeptidase 1
- EC
- 3.4.11.22
- UniProt
- P14904
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W, B, F, c, d, J, e, L, f, N, g, h, R, i, T, j, V, k, X, l | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 24 | 88% helix, 0% strand | P14904 |
| Y | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 20 | 85% helix, 0% strand | P14904 |
| a, b, H, P | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 23 | 91% helix, 0% strand | P14904 |
| D, m | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 22 | 91% helix, 0% strand | P14904 |
| Z | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 14 | 86% helix, 0% strand | P14904 |
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.83 | 0.84 | 109 | empty |
| 2 | 370 | 0.78 | 0.87 | 58 | empty |
| 3 | 580 | 0.71 | 0.79 | 70 | empty |
| 4 | 891 | 0.70 | 0.75 | 81 | empty |
| 5 | 59 | 0.65 | 0.94 | 17 | empty |
Interfaces
117 interfaces between chains.
- W–l · 556 Ų buried · 2 hydrogen bonds · protein-protein
- L–f · 533 Ų buried · 1 hydrogen bond · protein-protein
- H–d · 529 Ų buried · 2 hydrogen bonds · protein-protein
- U–k · 521 Ų buried · 0 hydrogen bonds · protein-protein
- Q–i · 509 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5JHC · Crystal structure of the self-assembled propeptides from Ape1 · the same entry in another collection · chain U against U, 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 P14904
- Elsewhere: RCSB PDB 5JHC · PDBe 5JHC · UniProt P14904
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