Research workbench
Crystal structure of putative NTF2-like transpeptidase (NP_281412.1) from campylobacter jejuni at 2.00 a resolution
Analyse Crystal structure of putative NTF2-like transpeptidase (NP_281412.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K7C
- Type
- protein
- Length
- 432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative NTF2-like transpeptidase
- UniProt
- Q0PBT7
- Ligands
- CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative NTF2-like transpeptidase | protein | 108 | 39% helix, 32% strand | Q0PBT7 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 13 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.72 | 0.79 | 59 | PEG, PGE |
| 2 | 410 | 0.63 | 0.77 | 35 | CL, PGE |
| 3 | 357 | 0.60 | 0.77 | 32 | PGE |
Interfaces
2 interfaces between chains.
- C–D · 442 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 418 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3K7C · Crystal structure of Putative NTF2-like transpeptidase (NP_281412.1) from CAMPYLOBACTER… · 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 Q0PBT7
- Elsewhere: RCSB PDB 3K7C · PDBe 3K7C · UniProt Q0PBT7
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