MolNFT v1 · #162424 · protein
Structure determination of the tetrahedral aminopeptidase TET2 from P. horikoshii by use of combined solid-state NMR, solution-state NMR and EM data 4.1 a, followed by REAL_SPACE_REFINEMENT at 4.1 a
6R8N: “Structure determination of the tetrahedral aminopeptidase TET2 from P. horikoshii by use of combined…”. Electron microscopy; solution nmr, 1 ligand (ZN), 20 pockets (best druggability 0.84). MolNFT v1 #162424 on GenesisL1: 3D…
- PDB
- 6R8N
- Type
- protein
- Length
- 4,236 residues
- Chains
- 12
- Method
- electron microscopy; solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrahedral aminopeptidase
- EC
- 3.4.11.-
- UniProt
- O59196
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy; solution nmr · 1 distinct chain · 27% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Tetrahedral aminopeptidase (EC 3.4.11.-) | protein | 353 | 27% helix, 18% strand | O59196 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, 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 | 1015 | 0.84 | 0.85 | 149 | empty |
| 2 | 356 | 0.76 | 0.86 | 52 | empty |
| 3 | 579 | 0.75 | 0.82 | 61 | empty |
| 4 | 484 | 0.75 | 0.84 | 65 | empty |
| 5 | 303 | 0.72 | 0.86 | 45 | empty |
Interfaces
42 interfaces between chains.
- J–L · 2652 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 2631 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 2629 Ų buried · 24 hydrogen bonds · protein-protein
- F–H · 2611 Ų buried · 24 hydrogen bonds · protein-protein
- I–K · 2603 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6R8N · Structure determination of the tetrahedral aminopeptidase TET2 from P. horikoshii by use… · the same entry in another collection · chain D against D, 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 O59196
- Elsewhere: RCSB PDB 6R8N · PDBe 6R8N · UniProt O59196
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