MolNFT v1 · #15799 · protein
X-ray structure of desulfovibrio desulfuricans bacterioferritin: the diiron centre in different catalytic states (as-isolated structure)
1NFV: “X-ray structure of desulfovibrio desulfuricans bacterioferritin: the diiron centre in different catalytic…”. X-ray diffraction, 4 ligands (FEC, 3PY, FE), 20 pockets (best druggability 0.80). MolNFT v1 #15799 on GenesisL1: 3D…
- PDB
- 1NFV
- Type
- protein
- Length
- 2,717 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterioferritin
- Ligands
- FEC, 3PY, FE, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, O | Bacterioferritin | protein | 169 | 76% helix, 1% strand | — |
| B, C, D, E, F, H, I, J, K, L, M, N, P | Bacterioferritin | protein | 170 | 76% helix, 0% 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
- 3PY · 3-hydroxypyruvic acid · ligand · chains D
- FE · Fe (III) 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 · 51 copies · chains A, B, G, N, C, D, E, F, M, H, I, J, K, P, L, O
- GOL · Glycerol · additive · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.80 | 0.89 | 34 | FEC |
| 2 | 882 | 0.80 | 0.82 | 98 | SO4, FEC |
| 3 | 915 | 0.79 | 0.81 | 99 | SO4, FEC |
| 4 | 832 | 0.78 | 0.82 | 98 | empty |
| 5 | 394 | 0.78 | 0.87 | 42 | FEC, SO4 |
Interfaces
31 interfaces between chains.
- I–J · 1806 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1795 Ų buried · 26 hydrogen bonds · protein-protein
- M–N · 1791 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1784 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1770 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 1NFV · X-ray structure of Desulfovibrio desulfuricans bacterioferritin: the diiron centre 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 1NFV · PDBe 1NFV
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