Research workbench
X-ray structure of the desulfovibrio desulfuricans bacterioferritin: the diiron site in different states (reduced structure)
Analyse X-ray structure of the desulfovibrio desulfuricans bacterioferritin: the diiron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NF4
- Type
- protein
- Length
- 2,709 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- Ligands
- FEC, FE2, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, J, K, N, O | Bacterioferritin | protein | 169 | 76% helix, 0% strand | — |
| H, I, L, M, P | Bacterioferritin | protein | 170 | 76% helix, 1% strand | — |
Ligands and binding sites
- FEC · 1,3,5,8-tetramethyl-porphine-2,4,6,7-tetrapropionic acid ferrous complex · ligand · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- FE2 · Fe (II) ion · metal · 32 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- SO4 · Sulfate ion · ion · 56 copies · chains A, B, G, N, C, D, E, F, H, I, J, K, L, M, O, P
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 | 931 | 0.81 | 0.82 | 89 | SO4, FEC |
| 2 | 519 | 0.78 | 0.85 | 46 | FEC, SO4 |
| 3 | 448 | 0.78 | 0.86 | 43 | FEC, SO4 |
| 4 | 541 | 0.78 | 0.84 | 46 | FEC, SO4 |
| 5 | 497 | 0.77 | 0.85 | 45 | FEC, SO4 |
Interfaces
30 interfaces between chains.
- K–L · 1743 Ų buried · 17 hydrogen bonds · protein-protein
- M–N · 1739 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1737 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1732 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1723 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1NF4 · X-Ray Structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in… · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 1NF4 · PDBe 1NF4
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