Research workbench
Structure of the ldtfm-avibactam carbamoyl enzyme
Analyse Structure of the ldtfm-avibactam carbamoyl enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FJ1
- Type
- protein
- Length
- 759 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L,D-transpeptidase
- UniProt
- A0A2D0BNR1
- Ligands
- P3G, NXL, CL
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | L,D-transpeptidase | protein | 253 | 24% helix, 36% strand | A0A2D0BNR1 |
Ligands and binding sites
- P3G · 3,6,9,12,15-pentaoxaheptadecane · ligand · 3 copies · chains A, B, C
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.73 | 0.76 | 109 | P3G, GOL, NXL |
| 2 | 990 | 0.73 | 0.76 | 83 | CL, P3G, GOL |
| 3 | 183 | 0.45 | 0.75 | 32 | NXL |
| 4 | 99 | 0.39 | 0.76 | 22 | NXL |
| 5 | 76 | 0.31 | 0.74 | 20 | GOL |
Interfaces
2 interfaces between chains.
- A–C · 636 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 618 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6FJ1 · Structure of the Ldtfm-avibactam carbamoyl enzyme · the same entry in another collection · chain C against C, 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 A0A2D0BNR1
- Elsewhere: RCSB PDB 6FJ1 · PDBe 6FJ1 · UniProt A0A2D0BNR1
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