MolNFT v1 · #94462 · protein
Pyrococcus horikoshii acylaminoacyl peptidase (orthorhombic crystal form)
4HXG · Putative uncharacterized protein PH0594: “Pyrococcus horikoshii acylaminoacyl peptidase (orthorhombic crystal form)”. X-ray diffraction, 2 ligands (MG, CL), 20 pockets (best druggability 0.78). MolNFT v1 #94462 on GenesisL1: 3D…
- PDB
- 4HXG
- Type
- protein
- Length
- 7,329 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein PH0594
- EC
- 3.4.19.1
- UniProt
- O58323
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 9 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein PH0594 (EC 3.4.19.1) | protein | 608 | 19% helix, 42% strand | O58323 |
| B, C, D | Putative uncharacterized protein PH0594 (EC 3.4.19.1) | protein | 612 | 19% helix, 42% strand | O58323 |
| E | Putative uncharacterized protein PH0594 (EC 3.4.19.1) | protein | 613 | 19% helix, 41% strand | O58323 |
| F | Putative uncharacterized protein PH0594 (EC 3.4.19.1) | protein | 614 | 19% helix, 40% strand | O58323 |
| G | Putative uncharacterized protein PH0594 (EC 3.4.19.1) | protein | 608 | 19% helix, 41% strand | O58323 |
| H | Putative uncharacterized protein PH0594 (EC 3.4.19.1) | protein | 609 | 19% helix, 41% strand | O58323 |
| I, L | Putative uncharacterized protein PH0594 (EC 3.4.19.1) | protein | 611 | 19% helix, 41% strand | O58323 |
| J | Putative uncharacterized protein PH0594 (EC 3.4.19.1) | protein | 609 | 19% helix, 40% strand | O58323 |
| K | Putative uncharacterized protein PH0594 (EC 3.4.19.1) | protein | 610 | 19% helix, 41% strand | O58323 |
Ligands and binding sites
- MG · Magnesium ion · metal · 21 copies · chains A, C, B, D, E, F, G, I, H, L, J
- CL · Chloride ion · ion · 2 copies · chains D, F, E
- HEZ · Hexane-1,6-diol · additive · 26 copies · chains A, B, E, C, D, F, G, H, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.78 | 0.80 | 99 | empty |
| 2 | 873 | 0.77 | 0.80 | 81 | HEZ, MG |
| 3 | 655 | 0.76 | 0.82 | 77 | HEZ, MG |
| 4 | 853 | 0.76 | 0.79 | 80 | HEZ, MG |
| 5 | 859 | 0.76 | 0.79 | 79 | HEZ, MG |
Interfaces
19 interfaces between chains.
- I–L · 2777 Ų buried · 51 hydrogen bonds · protein-protein
- B–E · 2764 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 2762 Ų buried · 49 hydrogen bonds · protein-protein
- C–F · 2666 Ų buried · 44 hydrogen bonds · protein-protein
- H–K · 2613 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 4HXG · Pyrococcus horikoshii acylaminoacyl peptidase (orthorhombic crystal form) · 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 O58323
- Elsewhere: RCSB PDB 4HXG · PDBe 4HXG · UniProt O58323
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