Research workbench
Crystal structure of serratia fonticola carbapenemase sfc-1
Analyse Crystal structure of serratia fonticola carbapenemase sfc-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EQI
- Type
- protein
- Length
- 545 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbapenem-hydrolizing beta-lactamase sfc-1
- EC
- 3.5.2.6
- UniProt
- Q6JP75
- Ligands
- NA
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbapenem-hydrolizing beta-lactamase sfc-1 (EC 3.5.2.6) | protein | 271 | 44% helix, 17% strand | Q6JP75 |
| B | Carbapenem-hydrolizing beta-lactamase sfc-1 (EC 3.5.2.6) | protein | 274 | 43% helix, 16% strand | Q6JP75 |
Ligands and binding sites
- NA · Sodium ion · metal · 22 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.71 | 0.86 | 23 | NA |
| 2 | 394 | 0.59 | 0.76 | 71 | NA |
| 3 | 87 | 0.43 | 0.79 | 25 | NA |
| 4 | 56 | 0.27 | 0.75 | 14 | EDO |
Interfaces
1 interface between chains.
- A–B · 767 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4EQI · Crystal structure of serratia fonticola carbapenemase SFC-1 · 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 Q6JP75
- Elsewhere: RCSB PDB 4EQI · PDBe 4EQI · UniProt Q6JP75
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