Research workbench
Structure of dps from microbacterium arborescens in the high iron form
Analyse Structure of dps from microbacterium arborescens in the high iron form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YJK
- Type
- protein
- Length
- 1,819 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Afp
- UniProt
- Q1X6M4
- Ligands
- OFE, FE
- Pockets
- 20 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 77% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Afp | protein | 149 | 79% helix, 3% strand | Q1X6M4 |
| B, D, E, F, H, K, L | Afp | protein | 152 | 75% helix, 3% strand | Q1X6M4 |
| C | Afp | protein | 157 | 74% helix, 3% strand | Q1X6M4 |
| G | Afp | protein | 153 | 76% helix, 3% strand | Q1X6M4 |
| I, J | Afp | protein | 148 | 79% helix, 3% strand | Q1X6M4 |
Ligands and binding sites
- OFE · Iron(II) oxide · ligand · 11 copies · chains A, B, C, I, D, J, E, F, H, G, K, L
- FE · Fe (III) ion · metal · 6 copies · chains B, D, L, A, C, E, G, I, K, H, F, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.62 | 0.89 | 16 | FE |
| 2 | 100 | 0.59 | 0.86 | 16 | FE |
| 3 | 356 | 0.59 | 0.77 | 48 | empty |
| 4 | 127 | 0.59 | 0.84 | 23 | FE |
| 5 | 293 | 0.57 | 0.77 | 36 | empty |
Interfaces
30 interfaces between chains.
- G–H · 1426 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1390 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1381 Ų buried · 22 hydrogen bonds · protein-protein
- D–J · 1360 Ų buried · 23 hydrogen bonds · protein-protein
- C–I · 1358 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2YJK · Structure of Dps from MICROBACTERIUM ARBORESCENS in the high iron form · 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
- Every structure of UniProt Q1X6M4
- Elsewhere: RCSB PDB 2YJK · PDBe 2YJK · UniProt Q1X6M4
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