Research workbench
Folding of an iron binding peptide in response to sedimentation is resolved using ferritin as a nano-reactor
Analyse Folding of an iron binding peptide in response to sedimentation is resolved… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZLQ
- Type
- protein
- Length
- 4,185 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferritin
- UniProt
- Q9CPX4
- Ligands
- FE
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z, A, C, E, G, J, K, M, P, R, S, T, W, D, F | Ferritin | protein | 174 | 76% helix, 1% strand | Q9CPX4 |
| H, I, L, N, O, Q, U, V, B | Ferritin | protein | 175 | 76% helix, 1% strand | Q9CPX4 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 16 copies · chains A, G, V, C, N, F, H, R, W, I, M, T, J, P, Q, E, O, B, K, S, U, Z, D, L
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 | 224 | 0.82 | 0.94 | 32 | empty |
| 2 | 229 | 0.81 | 0.93 | 29 | empty |
| 3 | 236 | 0.81 | 0.93 | 33 | empty |
| 4 | 236 | 0.80 | 0.93 | 30 | empty |
| 5 | 232 | 0.80 | 0.93 | 32 | empty |
Interfaces
72 interfaces between chains.
- M–N · 1474 Ų buried · 24 hydrogen bonds · protein-protein
- I–J · 1474 Ų buried · 15 hydrogen bonds · protein-protein
- V–W · 1464 Ų buried · 18 hydrogen bonds · protein-protein
- H–S · 1461 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1454 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6ZLQ · Folding of an iron binding peptide in response to sedimentation is resolved using… · the same entry in another collection · chain Z against Z, 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 Q9CPX4
- Elsewhere: RCSB PDB 6ZLQ · PDBe 6ZLQ · UniProt Q9CPX4
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