Research workbench
X-ray structure of dps from listeria monocytogenes
Analyse X-ray structure of dps from listeria monocytogenes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IY4
- Type
- protein
- Length
- 3,611 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-heme iron-containing ferritin
- UniProt
- Q8Y8G1
- Ligands
- FE
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, G, O, Q, R, S | Non-heme iron-containing ferritin | protein | 151 | 76% helix, 0% strand | Q8Y8G1 |
| B, D, E, H, I, J, K, L, N, P, T, V, X, Y | Non-heme iron-containing ferritin | protein | 150 | 75% helix, 0% strand | Q8Y8G1 |
| M | Non-heme iron-containing ferritin | protein | 149 | 75% helix, 0% strand | Q8Y8G1 |
| U | Non-heme iron-containing ferritin | protein | 154 | 73% helix, 0% strand | Q8Y8G1 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 24 copies · chains B, D, A, C, E, G, F, H, I, K, J, L, M, O, N, P, Q, S, R, T, U, X, V, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.85 | 0.87 | 86 | empty |
| 2 | 702 | 0.67 | 0.75 | 87 | FE |
| 3 | 688 | 0.66 | 0.75 | 80 | empty |
| 4 | 394 | 0.61 | 0.76 | 48 | empty |
| 5 | 429 | 0.61 | 0.76 | 47 | FE |
Interfaces
65 interfaces between chains.
- E–G · 1306 Ų buried · 17 hydrogen bonds · protein-protein
- U–X · 1291 Ų buried · 18 hydrogen bonds · protein-protein
- N–P · 1289 Ų buried · 17 hydrogen bonds · protein-protein
- I–K · 1289 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1281 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2IY4 · X-ray structure of Dps from Listeria monocytogenes · 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 Q8Y8G1
- Elsewhere: RCSB PDB 2IY4 · PDBe 2IY4 · UniProt Q8Y8G1
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