Research workbench
Structure of an engineered bacterial microcompartment shell protein binding a [4Fe-4S] cluster
Analyse Structure of an engineered bacterial microcompartment shell protein binding a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DII
- Type
- protein
- Length
- 1,180 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.804
- Source
- Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2)
- Molecule
- Microcompartments protein
- UniProt
- D0LHE3
- Ligands
- SF4
- Pockets
- 16 · best druggability 0.47
Structure
x-ray diffraction · resolution 1.804 · 6 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Microcompartments protein | protein | 194 | 35% helix, 30% strand | D0LHE3 |
| B | Microcompartments protein | protein | 196 | 33% helix, 30% strand | D0LHE3 |
| C | Microcompartments protein | protein | 199 | 36% helix, 30% strand | D0LHE3 |
| D | Microcompartments protein | protein | 199 | 34% helix, 30% strand | D0LHE3 |
| E | Microcompartments protein | protein | 195 | 33% helix, 30% strand | D0LHE3 |
| F | Microcompartments protein | protein | 197 | 36% helix, 30% strand | D0LHE3 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.47 | 0.83 | 14 | empty |
| 2 | 93 | 0.46 | 0.80 | 18 | empty |
| 3 | 77 | 0.46 | 0.82 | 17 | empty |
| 4 | 111 | 0.44 | 0.78 | 30 | empty |
| 5 | 69 | 0.40 | 0.80 | 15 | empty |
Interfaces
7 interfaces between chains.
- B–C · 991 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 897 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 885 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 885 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 870 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5DII · Structure of an engineered bacterial microcompartment shell protein binding a [4FE-4S]… · the same entry in another collection · chain F against F, TM-score 1.00
- D0LHE3 · AlphaFold monomer V2.0 prediction for bacterial microcompartment protein trimer-1 (D0LHE3) · a predicted model of the same protein · chain C 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 D0LHE3
- Elsewhere: RCSB PDB 5DII · PDBe 5DII · UniProt D0LHE3
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