Research workbench
Crystal structure of NE2512 protein of unknown function from nitrosomonas europaea
Analyse Crystal structure of NE2512 protein of unknown function from nitrosomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PD1
- Type
- protein
- Length
- 405 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q82S47
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 103 | 35% helix, 36% strand | Q82S47 |
| B | Hypothetical protein | protein | 100 | 36% helix, 37% strand | Q82S47 |
| C, D | Hypothetical protein | protein | 101 | 37% helix, 38% strand | Q82S47 |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.84 | 0.95 | 41 | ACT |
| 2 | 322 | 0.61 | 0.79 | 37 | empty |
| 3 | 103 | 0.60 | 0.86 | 20 | empty |
| 4 | 96 | 0.57 | 0.85 | 18 | ACT |
| 5 | 76 | 0.33 | 0.75 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1504 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1478 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 668 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 58 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 36 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2PD1 · Crystal structure of NE2512 protein of unknown function from Nitrosomonas europaea · 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 Q82S47
- Elsewhere: RCSB PDB 2PD1 · PDBe 2PD1 · UniProt Q82S47
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