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Structure of a modified mouse H-chain ferritin with a lanthanide binding motif
Analyse Structure of a modified mouse H-chain ferritin with a lanthanide binding motif in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OBA
- Type
- protein
- Length
- 4,155 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin heavy chain
- EC
- 1.16.3.1
- UniProt
- P09528
- Ligands
- FE
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, H, I, K, M, O, P, Q, T, U, W | Ferritin heavy chain (EC 1.16.3.1) | protein | 173 | 73% helix, 1% strand | P09528 |
| F, G, L, R, S, V, X | Ferritin heavy chain (EC 1.16.3.1) | protein | 174 | 72% helix, 1% strand | P09528 |
| J, N | Ferritin heavy chain (EC 1.16.3.1) | protein | 171 | 72% helix, 1% strand | P09528 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 32 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.79 | 0.99 | 18 | empty |
| 2 | 65 | 0.76 | 0.99 | 15 | empty |
| 3 | 69 | 0.75 | 0.99 | 15 | empty |
| 4 | 70 | 0.75 | 0.98 | 14 | empty |
| 5 | 56 | 0.75 | 1.00 | 15 | empty |
Interfaces
72 interfaces between chains.
- N–Q · 1617 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 1591 Ų buried · 28 hydrogen bonds · protein-protein
- O–V · 1590 Ų buried · 31 hydrogen bonds · protein-protein
- C–J · 1589 Ų buried · 31 hydrogen bonds · protein-protein
- L–S · 1589 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5OBA · Structure of a modified mouse H-chain ferritin with a lanthanide binding motif · the same entry in another collection · chain J against J, 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 P09528
- Elsewhere: RCSB PDB 5OBA · PDBe 5OBA · UniProt P09528
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