MolNFT v1 · #64574 · protein
Native phpd with cadmium atoms
3G7D: “Native phpd with cadmium atoms”. X-ray diffraction, 1 ligand (CD), 6 pockets (best druggability 0.48). MolNFT v1 #64574 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3G7D
- Type
- protein
- Length
- 418 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phpd
- UniProt
- Q5IW40
- Ligands
- CD
- Pockets
- 6 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phpd | protein | 418 | 31% helix, 27% strand | Q5IW40 |
Ligands and binding sites
- CD · Cadmium ion · metal · 13 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.48 | 0.78 | 19 | CD |
| 2 | 170 | 0.46 | 0.76 | 28 | empty |
| 3 | 71 | 0.40 | 0.79 | 19 | empty |
| 4 | 57 | 0.34 | 0.78 | 17 | empty |
| 5 | 53 | 0.33 | 0.77 | 21 | empty |
Modifications
Observed in the structure: 5 modified (engineered).
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 Q5IW40
- Elsewhere: RCSB PDB 3G7D · PDBe 3G7D · UniProt Q5IW40
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