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Crystal structure of a protein with unknown function from DUF155 family (YP_292156.1) from prochlorococcus sp. NATL2A at 1.80 a resolution
Analyse Crystal structure of a protein with unknown function from DUF155 family… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IT9
- Type
- protein
- Length
- 482 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q46J75
- Ligands
- CL
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 120 | 27% helix, 42% strand | Q46J75 |
| B, C | Hypothetical protein | protein | 120 | 29% helix, 41% strand | Q46J75 |
| D | Hypothetical protein | protein | 122 | 30% helix, 39% strand | Q46J75 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.65 | 0.77 | 55 | EDO |
| 2 | 107 | 0.43 | 0.78 | 23 | empty |
| 3 | 79 | 0.37 | 0.77 | 21 | empty |
| 4 | 78 | 0.37 | 0.77 | 20 | empty |
| 5 | 50 | 0.32 | 0.78 | 18 | empty |
Interfaces
4 interfaces between chains.
- C–D · 976 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 921 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 257 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 198 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 2IT9 · Crystal structure of a protein with unknown function from DUF155 family (YP_292156.1)… · 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 Q46J75
- Elsewhere: RCSB PDB 2IT9 · PDBe 2IT9 · UniProt Q46J75
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