MolNFT v1 · #116592 · protein
Structure of haliangium ochraceum bmc-T ho-5812
5DIH · Microcompartments protein: “Structure of haliangium ochraceum bmc-T ho-5812”. X-ray diffraction, 7 pockets (best druggability 0.66). MolNFT v1 #116592 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DIH
- Type
- protein
- Length
- 1,160 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Microcompartments protein
- UniProt
- D0LHE3
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Microcompartments protein | protein | 201 | 34% helix, 28% strand | D0LHE3 |
| B | Microcompartments protein | protein | 202 | 35% helix, 29% strand | D0LHE3 |
| C | Microcompartments protein | protein | 191 | 31% helix, 31% strand | D0LHE3 |
| D | Microcompartments protein | protein | 182 | 34% helix, 31% strand | D0LHE3 |
| E | Microcompartments protein | protein | 192 | 32% helix, 31% strand | D0LHE3 |
| F | Microcompartments protein | protein | 192 | 33% helix, 31% strand | D0LHE3 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.66 | 0.78 | 83 | empty |
| 2 | 363 | 0.65 | 0.79 | 81 | empty |
| 3 | 402 | 0.54 | 0.73 | 41 | empty |
| 4 | 99 | 0.48 | 0.81 | 20 | empty |
| 5 | 78 | 0.38 | 0.77 | 19 | empty |
Interfaces
9 interfaces between chains.
- B–D · 1038 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 908 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 897 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 879 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 858 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5DIH · Structure of Haliangium ochraceum BMC-T HO-5812 · 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 0.99
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 5DIH · PDBe 5DIH · UniProt D0LHE3
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