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Crystal structure of N-terminal domain (CREATINASE/PROLIDASE like domain) of putative metallopeptidase from corynebacterium diphtheriae
Analyse Crystal structure of N-terminal domain (CREATINASE/PROLIDASE like domain) of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QOC
- Type
- protein
- Length
- 507 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative metallopeptidase
- UniProt
- Q6NH06
- Ligands
- SO4, CL
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative metallopeptidase | protein | 129 | 39% helix, 24% strand | Q6NH06 |
| B | Putative metallopeptidase | protein | 126 | 36% helix, 25% strand | Q6NH06 |
| C | Putative metallopeptidase | protein | 128 | 41% helix, 23% strand | Q6NH06 |
| D | Putative metallopeptidase | protein | 124 | 36% helix, 23% strand | Q6NH06 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, D, B, C
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.69 | 0.77 | 83 | empty |
| 2 | 295 | 0.57 | 0.77 | 27 | empty |
| 3 | 175 | 0.55 | 0.79 | 23 | empty |
| 4 | 61 | 0.45 | 0.83 | 16 | empty |
| 5 | 60 | 0.37 | 0.79 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–D · 348 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 339 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 313 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 311 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 306 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3QOC · Crystal structure of N-terminal domain (Creatinase/Prolidase like domain) of putative… · 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 Q6NH06
- Elsewhere: RCSB PDB 3QOC · PDBe 3QOC · UniProt Q6NH06
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