Research workbench
Crystal structure of protein of unknown function SO2669 from shewanella oneidensis mr-1
Analyse Crystal structure of protein of unknown function SO2669 from shewanella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NR5
- Type
- protein
- Length
- 489 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein SO2669
- UniProt
- Q8EDS4
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 7 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein SO2669 | protein | 60 | 75% helix, 0% strand | Q8EDS4 |
| B | Hypothetical protein SO2669 | protein | 58 | 74% helix, 0% strand | Q8EDS4 |
| C, H | Hypothetical protein SO2669 | protein | 64 | 75% helix, 0% strand | Q8EDS4 |
| D | Hypothetical protein SO2669 | protein | 63 | 73% helix, 0% strand | Q8EDS4 |
| F | Hypothetical protein SO2669 | protein | 57 | 75% helix, 0% strand | Q8EDS4 |
| G | Hypothetical protein SO2669 | protein | 58 | 78% helix, 0% strand | Q8EDS4 |
| E | Hypothetical protein SO2669 | protein | 65 | 66% helix, 0% strand | Q8EDS4 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains B, D, G, F, C, A, H
- ACT · Acetate ion · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.62 | 0.76 | 38 | MPD |
| 2 | 113 | 0.38 | 0.75 | 19 | empty |
| 3 | 97 | 0.34 | 0.74 | 16 | empty |
| 4 | 70 | 0.32 | 0.75 | 13 | MPD |
| 5 | 56 | 0.30 | 0.76 | 15 | empty |
Interfaces
10 interfaces between chains.
- A–H · 1544 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1446 Ų buried · 17 hydrogen bonds · protein-protein
- D–G · 1371 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 909 Ų buried · 16 hydrogen bonds · protein-protein
- B–G · 847 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 2NR5 · Crystal Structure of Protein of Unknown Function SO2669 from Shewanella oneidensis MR-1 · 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 Q8EDS4
- Elsewhere: RCSB PDB 2NR5 · PDBe 2NR5 · UniProt Q8EDS4
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