Research workbench
Crystal structure of aminopeptidase from marine sediment archaeon thaumarchaeota archaeon
Analyse Crystal structure of aminopeptidase from marine sediment archaeon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PF1
- Type
- protein
- Length
- 2,442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase S15/COCE/NOND
- UniProt
- M7TVE7
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Peptidase S15/COCE/NOND | protein | 611 | 22% helix, 28% strand | M7TVE7 |
| B, C | Peptidase S15/COCE/NOND | protein | 610 | 23% helix, 29% strand | M7TVE7 |
Ligands and binding sites
- GOL · Glycerol · additive · 15 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C, D
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 | 816 | 0.77 | 0.81 | 86 | GOL |
| 2 | 941 | 0.76 | 0.79 | 83 | GOL |
| 3 | 984 | 0.74 | 0.77 | 87 | empty |
| 4 | 890 | 0.74 | 0.78 | 80 | empty |
| 5 | 740 | 0.73 | 0.78 | 85 | GOL |
Interfaces
6 interfaces between chains.
- A–C · 2048 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 2034 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1406 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1330 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 806 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4PF1 · Crystal structure of aminopeptidase from marine sediment archaeon Thaumarchaeota archaeon · 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 M7TVE7
- Elsewhere: RCSB PDB 4PF1 · PDBe 4PF1 · UniProt M7TVE7
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