MolNFT v1 · #155360 · protein
Recombinant tegillarca granosa ferritin
6L55: “Recombinant tegillarca granosa ferritin”. X-ray diffraction, 2 ligands (FE, NA), 10 pockets (best druggability 0.75). MolNFT v1 #155360 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6L55
- Type
- protein
- Length
- 2,031 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- EC
- 1.16.3.1
- UniProt
- D3JCC5
- Ligands
- FE, NA
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, H, I, K, L | Ferritin (EC 1.16.3.1) | protein | 169 | 73% helix, 1% strand | D3JCC5 |
| C, F, J | Ferritin (EC 1.16.3.1) | protein | 170 | 73% helix, 1% strand | D3JCC5 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 16 copies · chains A, B, C, D, H, E, F, G, I, J, K, L
- NA · Sodium ion · metal · 11 copies · chains A, B, C, E, D, F, G, H, K
- FMT · Formic acid · additive · 9 copies · chains A, B, C, F, G, H, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.75 | 0.99 | 14 | empty |
| 2 | 60 | 0.74 | 0.99 | 14 | empty |
| 3 | 54 | 0.74 | 1.00 | 13 | empty |
| 4 | 54 | 0.73 | 0.99 | 13 | empty |
| 5 | 56 | 0.73 | 0.99 | 13 | empty |
Interfaces
13 interfaces between chains.
- C–J · 1670 Ų buried · 28 hydrogen bonds · protein-protein
- F–G · 1662 Ų buried · 30 hydrogen bonds · protein-protein
- D–I · 1655 Ų buried · 27 hydrogen bonds · protein-protein
- K–L · 1649 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1643 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6L55 · Recombinant Tegillarca granosa ferritin · the same entry in another collection · chain E against E, 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 D3JCC5
- Elsewhere: RCSB PDB 6L55 · PDBe 6L55 · UniProt D3JCC5
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