MolNFT v1 · #136320 · protein
Crystal structure of zn-bound human heavy-chain ferritin variant 122H- delta C-star with para-xylenedihydroxamate
5UP9 · Ferritin heavy chain: “Crystal structure of zn-bound human heavy-chain ferritin variant 122H- delta C-star with…”. X-ray diffraction, 2 ligands (BYX, ZN), 11 pockets (best druggability 0.75). MolNFT v1 #136320 on GenesisL1: 3D…
- PDB
- 5UP9
- Type
- protein
- Length
- 1,039 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin heavy chain
- EC
- 1.16.3.1
- UniProt
- P02794
- Ligands
- BYX, ZN
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferritin heavy chain (EC 1.16.3.1) | protein | 172 | 72% helix, 1% strand | P02794 |
| B, F | Ferritin heavy chain (EC 1.16.3.1) | protein | 174 | 72% helix, 1% strand | P02794 |
| C, E | Ferritin heavy chain (EC 1.16.3.1) | protein | 173 | 72% helix, 1% strand | P02794 |
| D | Ferritin heavy chain (EC 1.16.3.1) | protein | 173 | 72% helix, 1% strand | P02794 |
Ligands and binding sites
- BYX · 2,2'-(1,4-phenylene)bis(N-hydroxyacetamide) · ligand · chains B, F
- ZN · Zinc ion · metal · 19 copies · chains A, D, E, F, B, C
- PEG · Di(hydroxyethyl)ether · additive · 19 copies · chains A, B, C, D, E, F
- PGE · Triethylene glycol · additive · 5 copies · chains A, B, D, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.75 | 0.99 | 16 | empty |
| 2 | 256 | 0.55 | 0.77 | 37 | empty |
| 3 | 67 | 0.44 | 0.82 | 18 | ZN |
| 4 | 110 | 0.43 | 0.78 | 22 | empty |
| 5 | 75 | 0.42 | 0.80 | 16 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1570 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1561 Ų buried · 30 hydrogen bonds · protein-protein
- C–E · 792 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 757 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 579 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5UP9 · Crystal Structure of Zn-bound Human Heavy-Chain ferritin variant 122H-delta C-star with… · the same entry in another collection · chain F against F, TM-score 1.00
- P02794 · AlphaFold monomer V2.0 prediction for ferritin heavy chain (P02794) · a predicted model of the same protein · chain D 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 5UP9 · PDBe 5UP9 · UniProt P02794
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