MolNFT v1 · #165817 · protein
Hcov-229E rbd class V in complex with human apn
6U7G · Aminopeptidase N: “Hcov-229E rbd class V in complex with human apn”. X-ray diffraction, 2 ligands (NAG, ZN), 18 pockets (best druggability 0.79). MolNFT v1 #165817 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6U7G
- Type
- protein
- Length
- 2,027 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N; Spike protein
- EC
- 3.4.11.2
- UniProt
- P15144, H1AG31
- Ligands
- NAG, ZN
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 898 | 46% helix, 20% strand | P15144 |
| B | Aminopeptidase N (EC 3.4.11.2) | protein | 899 | 47% helix, 20% strand | P15144 |
| C | Spike protein | protein | 119 | 0% helix, 50% strand | H1AG31 |
| D | Spike protein | protein | 111 | 0% helix, 50% strand | H1AG31 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.79 | 0.81 | 70 | empty |
| 2 | 368 | 0.73 | 0.84 | 49 | empty |
| 3 | 287 | 0.73 | 0.86 | 44 | empty |
| 4 | 579 | 0.72 | 0.81 | 69 | empty |
| 5 | 350 | 0.72 | 0.84 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1031 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 535 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 510 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
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 P15144
- Every structure of UniProt H1AG31
- Elsewhere: RCSB PDB 6U7G · PDBe 6U7G · UniProt P15144 · UniProt H1AG31
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