MolNFT v1 · #159240 · protein
X-ray crystal structure of the ectodomain of the toxoplasma gondii ME49 aminopeptidase N (TGME49_224350)
6OIU: “X-ray crystal structure of the ectodomain of the toxoplasma gondii ME49 aminopeptidase N (TGME49_224350)”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.84). MolNFT v1 #159240 on GenesisL1: 3D structure, binding…
- PDB
- 6OIU
- Type
- protein
- Length
- 3,575 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- S8G5K8
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 890 | 43% helix, 22% strand | S8G5K8 |
| B | Aminopeptidase N (EC 3.4.11.2) | protein | 899 | 43% helix, 22% strand | S8G5K8 |
| C | Aminopeptidase N (EC 3.4.11.2) | protein | 900 | 43% helix, 22% strand | S8G5K8 |
| D | Aminopeptidase N (EC 3.4.11.2) | protein | 886 | 44% helix, 22% strand | S8G5K8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 9 copies · chains A, B, C
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 | 1048 | 0.84 | 0.85 | 93 | ZN, GOL |
| 2 | 882 | 0.84 | 0.85 | 86 | empty |
| 3 | 854 | 0.83 | 0.85 | 76 | ZN, GOL |
| 4 | 1171 | 0.83 | 0.84 | 97 | empty |
| 5 | 751 | 0.81 | 0.85 | 75 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1250 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 665 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 629 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 169 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6OIU · X-ray crystal structure of the ectodomain of the Toxoplasma gondii ME49 Aminopeptidase N… · the same entry in another collection · chain B against B, 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 S8G5K8
- Elsewhere: RCSB PDB 6OIU · PDBe 6OIU · UniProt S8G5K8
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