Research workbench
Crystal structure of a a marine metagenome protein (JCVI_PEP_1096685590403) from uncultured marine organism at 2.53 a resolution
Analyse Crystal structure of a a marine metagenome protein (JCVI_PEP_1096685590403)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PGC
- Type
- protein
- Length
- 1,024 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- Ligands
- CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 206 | 39% helix, 33% strand | — |
| B, D, E | Uncharacterized protein | protein | 205 | 39% helix, 33% strand | — |
| C | Uncharacterized protein | protein | 203 | 39% helix, 33% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.77 | 0.97 | 22 | CL |
| 2 | 90 | 0.76 | 0.97 | 21 | empty |
| 3 | 82 | 0.76 | 0.98 | 22 | CL |
| 4 | 83 | 0.75 | 0.97 | 24 | CL |
| 5 | 90 | 0.75 | 0.97 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1073 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1058 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 969 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 887 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 865 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 2PGC · Crystal structure of a a marine metagenome protein (jcvi_pep_1096685590403) from… · 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
- Elsewhere: RCSB PDB 2PGC · PDBe 2PGC
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.