MolNFT v1 · #129133 · protein
Structure of a modified mouse H chain ferritin with a lanthanide binding motif in complex with terbium
5OBB · Ferritin heavy chain: “Structure of a modified mouse H chain ferritin with a lanthanide binding motif in complex with terbium”. X-ray diffraction, 1 ligand (TB), 20 pockets (best druggability 0.74). MolNFT v1 #129133 on GenesisL1…
- PDB
- 5OBB
- Type
- protein
- Length
- 4,177 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
- TB
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, G, H, I, J, K, O, P, R, U, W | Ferritin heavy chain (EC 1.16.3.1) | protein | 174 | 74% helix, 1% strand | P09528 |
| C, D, E, N | Ferritin heavy chain (EC 1.16.3.1) | protein | 173 | 74% helix, 1% strand | P09528 |
| L, M, Q, S, X | Ferritin heavy chain (EC 1.16.3.1) | protein | 175 | 73% helix, 1% strand | P09528 |
| T | Ferritin heavy chain (EC 1.16.3.1) | protein | 176 | 72% helix, 1% strand | P09528 |
| V | Ferritin heavy chain (EC 1.16.3.1) | protein | 172 | 73% helix, 1% strand | P09528 |
Ligands and binding sites
- TB · Terbium(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 | 60 | 0.74 | 0.99 | 15 | empty |
| 2 | 811 | 0.73 | 0.78 | 96 | empty |
| 3 | 53 | 0.71 | 0.98 | 14 | empty |
| 4 | 694 | 0.71 | 0.78 | 87 | empty |
| 5 | 326 | 0.68 | 0.82 | 40 | empty |
Interfaces
72 interfaces between chains.
- H–K · 1609 Ų buried · 25 hydrogen bonds · protein-protein
- P–U · 1601 Ų buried · 26 hydrogen bonds · protein-protein
- C–J · 1599 Ų buried · 24 hydrogen bonds · protein-protein
- O–V · 1598 Ų buried · 26 hydrogen bonds · protein-protein
- T–W · 1598 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5OBB · Structure of a modified mouse H chain ferritin with a lanthanide binding motif in complex… · the same entry in another collection · chain I against I, 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 5OBB · PDBe 5OBB · UniProt P09528
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