MolNFT v2 · #116913 · protein
Structure of the Haliangium ochraceum BMC-H shell protein
5DJB · Microcompartments protein: “Structure of the Haliangium ochraceum BMC-H shell protein”. X-ray diffraction at 1.798, 4 pockets (best druggability 0.63). MolNFT v2 #116913 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DJB
- Type
- protein
- Length
- 765 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.798
- Source
- Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2)
- Molecule
- Microcompartments protein
- UniProt
- D0LID5
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · resolution 1.798 · 3 distinct chains · 37% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Microcompartments protein | protein | 98 | 36% helix, 34% strand | D0LID5 |
| C | Microcompartments protein | protein | 95 | 37% helix, 35% strand | D0LID5 |
| E, F, G, H | Microcompartments protein | protein | 94 | 37% helix, 34% strand | D0LID5 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.63 | 0.74 | 56 | empty |
| 2 | 66 | 0.31 | 0.75 | 14 | empty |
| 3 | 83 | 0.29 | 0.72 | 20 | empty |
| 4 | 60 | 0.24 | 0.71 | 16 | empty |
Interfaces
10 interfaces between chains.
- C–D · 957 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 954 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 947 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 940 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 348 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5DJB · Structure of the haliangium ochraceum bmc-H shell protein · the same entry in another collection · chain H against H, TM-score 1.00
- D0LID5 · AlphaFold monomer V2.0 prediction for bacterial microcompartment protein homohexamer… · a predicted model of the same protein · chain H against A, TM-score 0.98
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 D0LID5
- Elsewhere: RCSB PDB 5DJB · PDBe 5DJB · UniProt D0LID5
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