Research workbench
Crystal structure of glycoprotein endopeptidase (TM0874) from thermotoga maritima at 2.50 a resolution
Analyse Crystal structure of glycoprotein endopeptidase (TM0874) from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A6A
- Type
- protein
- Length
- 381 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein TM0874
- Ligands
- UNL
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein TM0874 | protein | 193 | 40% helix, 32% strand | — |
| B | Hypothetical protein TM0874 | protein | 188 | 38% helix, 36% strand | — |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.61 | 0.80 | 46 | empty |
| 2 | 248 | 0.55 | 0.77 | 36 | UNL |
| 3 | 184 | 0.53 | 0.78 | 29 | UNL |
| 4 | 170 | 0.45 | 0.75 | 24 | empty |
| 5 | 93 | 0.32 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1289 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2A6A · Crystal structure of Glycoprotein endopeptidase (tm0874) from THERMOTOGA MARITIMA at 2.50… · 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 2A6A · PDBe 2A6A
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