MolNFT v1 · #155975 · protein
Structure of sinonovacula constricta ferritin
6LP5: “Structure of sinonovacula constricta ferritin”. X-ray diffraction, 2 ligands (FE, FE2), 11 pockets (best druggability 0.78). MolNFT v1 #155975 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6LP5
- Type
- protein
- Length
- 1,020 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- EC
- 1.16.3.1
- UniProt
- D2JIV0
- Ligands
- FE, FE2
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Ferritin (EC 1.16.3.1) | protein | 170 | 74% helix, 1% strand | D2JIV0 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F
- FE2 · Fe (II) ion · metal · 2 copies · chains A, F
- HEZ · Hexane-1,6-diol · additive · 7 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.78 | 0.98 | 19 | HEZ |
| 2 | 179 | 0.71 | 0.89 | 31 | empty |
| 3 | 142 | 0.71 | 0.90 | 28 | HEZ |
| 4 | 764 | 0.70 | 0.77 | 72 | empty |
| 5 | 150 | 0.52 | 0.79 | 22 | empty |
Interfaces
7 interfaces between chains.
- C–E · 1315 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1310 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1301 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 677 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 552 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6LP5 · Structure of Sinonovacula constricta ferritin · 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 D2JIV0
- Elsewhere: RCSB PDB 6LP5 · PDBe 6LP5 · UniProt D2JIV0
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