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Structure of a glutamine donor mimicking inhibitory peptide shaped by the catalytic cleft of microbial transglutaminase
Analyse Structure of a glutamine donor mimicking inhibitory peptide shaped by the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GMG
- Type
- protein
- Length
- 678 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Streptomyces mobaraensis NBRC 13819 = DSM 40847; SYNTHETIC CONSTRUCT
- Molecule
- Protein-glutamine gamma-glutamyltransferase; Papain inhibitor
- UniProt
- M3C567
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.25 · 4 distinct chains · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-glutamine gamma-glutamyltransferase | protein | 331 | 32% helix, 17% strand | M3C567 |
| B | Protein-glutamine gamma-glutamyltransferase | protein | 330 | 33% helix, 16% strand | M3C567 |
| C | Papain inhibitor | protein | 8 | 0% helix, 0% strand | — |
| D | Papain inhibitor | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, C, B
- FLC · Citrate anion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.75 | 0.78 | 103 | empty |
| 2 | 250 | 0.68 | 0.84 | 44 | FLC |
| 3 | 73 | 0.44 | 0.81 | 26 | PEG |
| 4 | 72 | 0.41 | 0.80 | 23 | PEG |
| 5 | 67 | 0.39 | 0.79 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 536 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 508 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 449 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6GMG · Structure of a glutamine donor mimicking inhibitory peptide shaped by the catalytic cleft… · 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 M3C567
- Elsewhere: RCSB PDB 6GMG · PDBe 6GMG · UniProt M3C567
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