MolNFT v1 · #189480 · protein
Apostichopus japonicus ferritin
7VHR: “Apostichopus japonicus ferritin”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.75). MolNFT v1 #189480 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VHR
- Type
- protein
- Length
- 4,049 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- EC
- 1.16.3.1
- UniProt
- Q2QJV4
- Ligands
- MG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H, L, M, N, O, S, U, X | Ferritin (EC 1.16.3.1) | protein | 168 | 74% helix, 1% strand | Q2QJV4 |
| B | Ferritin (EC 1.16.3.1) | protein | 171 | 74% helix, 1% strand | Q2QJV4 |
| D, E, G, I, K, P, R, T, V, W | Ferritin (EC 1.16.3.1) | protein | 169 | 73% helix, 1% strand | Q2QJV4 |
| F, Q | Ferritin (EC 1.16.3.1) | protein | 169 | 73% helix, 1% strand | Q2QJV4 |
| J | Ferritin (EC 1.16.3.1) | protein | 170 | 74% helix, 1% strand | Q2QJV4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 40 copies · chains A, F, G, B, C, I, D, K, M, E, L, O, H, R, S, J, V, X, N, U, P, T, W, Q
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 | 74 | 0.75 | 0.98 | 13 | empty |
| 2 | 78 | 0.75 | 0.97 | 14 | empty |
| 3 | 70 | 0.75 | 0.98 | 14 | empty |
| 4 | 89 | 0.74 | 0.96 | 18 | empty |
| 5 | 110 | 0.74 | 0.94 | 20 | empty |
Interfaces
72 interfaces between chains.
- E–F · 1576 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1573 Ų buried · 39 hydrogen bonds · protein-protein
- S–T · 1565 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 1559 Ų buried · 31 hydrogen bonds · protein-protein
- U–V · 1554 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 7VHR · Apostichopus japonicus ferritin · 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 Q2QJV4
- Elsewhere: RCSB PDB 7VHR · PDBe 7VHR · UniProt Q2QJV4
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