Research workbench
Crystal structure of efi-502318, an enolase family member from agrobacterium tumefaciens with homology to dipeptide epimerases (bound sodium, L-ala-L-glu with ordered loop)
Analyse Crystal structure of efi-502318, an enolase family member from agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GFI
- Type
- protein
- Length
- 1,312 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme family protein
- UniProt
- A9CIT6
- Ligands
- NA, CL, SO4
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing enzyme family protein | protein | 327 | 37% helix, 23% strand | A9CIT6 |
| B, D | Mandelate RACEMASE/MUCONATE lactonizing enzyme family protein | protein | 328 | 36% helix, 23% strand | A9CIT6 |
| C | Mandelate RACEMASE/MUCONATE lactonizing enzyme family protein | protein | 329 | 36% helix, 23% strand | A9CIT6 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 5 copies · chains B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains B, C, A, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.77 | 0.80 | 110 | CL |
| 2 | 146 | 0.56 | 0.82 | 27 | empty |
| 3 | 313 | 0.54 | 0.75 | 34 | empty |
| 4 | 104 | 0.47 | 0.80 | 18 | empty |
| 5 | 98 | 0.45 | 0.79 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–C · 835 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 807 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 386 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 370 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 370 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4GFI · Crystal structure of EFI-502318, an enolase family member from Agrobacterium tumefaciens… · 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 A9CIT6
- Elsewhere: RCSB PDB 4GFI · PDBe 4GFI · UniProt A9CIT6
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