Research workbench
Crystal structure of human H-chain ferritin variant 157C delta C-star modified with a raft agent
Analyse Crystal structure of human H-chain ferritin variant 157C delta C-star modified… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WYG
- Type
- protein
- Length
- 688 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin heavy chain
- EC
- 1.16.3.1
- UniProt
- P02794
- Ligands
- RFT, FE, CA
- Pockets
- 7 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ferritin heavy chain (EC 1.16.3.1) | protein | 172 | 72% helix, 0% strand | P02794 |
Ligands and binding sites
- RFT · butyl 1-{[2-(2,5-dioxopyrrolidin-1-yl)ethyl]amino}-2-methyl-1-oxopropan-2-yl carbonotrithioate · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 9 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.38 | 0.80 | 16 | empty |
| 2 | 56 | 0.35 | 0.78 | 17 | RFT |
| 3 | 60 | 0.33 | 0.76 | 14 | empty |
| 4 | 70 | 0.33 | 0.76 | 20 | empty |
| 5 | 65 | 0.32 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 526 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 515 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 514 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 513 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6WYG · Crystal structure of Human H-chain Ferritin variant 157C Delta C-star Modified with a… · the same entry in another collection · chain D against D, TM-score 1.00
- P02794 · AlphaFold monomer V2.0 prediction for ferritin heavy chain (P02794) · a predicted model of the same protein · 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 P02794
- Elsewhere: RCSB PDB 6WYG · PDBe 6WYG · UniProt P02794
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.