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Crystal structure of enolase BRADO_4202 (target efi-501651) from bradyrhizobium sp. ORS278 with calcium and acetate bound
Analyse Crystal structure of enolase BRADO_4202 (target efi-501651) from bradyrhizobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TOY
- Type
- protein
- Length
- 1,436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing enzyme family protein
- EC
- 5.1.2.2, 5.5.1.1
- UniProt
- A4YVM8
- Ligands
- CA, NI
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mandelate RACEMASE/MUCONATE lactonizing enzyme family protein (EC 5.1.2.2, 5.5.1.1) | protein | 359 | 42% helix, 23% strand | A4YVM8 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, C, B, D
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C, D
- P4C · O-acetaldehydyl-hexaethylene glycol · additive · 6 copies · chains A, B, D, C
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.87 | 0.89 | 88 | P4C |
| 2 | 839 | 0.83 | 0.85 | 81 | P4C |
| 3 | 53 | 0.69 | 0.97 | 22 | ACT |
| 4 | 547 | 0.68 | 0.78 | 65 | CA, P4C |
| 5 | 197 | 0.66 | 0.84 | 33 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1779 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 973 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 940 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 235 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 224 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3TOY · CRYSTAL STRUCTURE OF ENOLASE BRADO_4202 (TARGET EFI-501651) FROM Bradyrhizobium sp.… · 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 A4YVM8
- Elsewhere: RCSB PDB 3TOY · PDBe 3TOY · UniProt A4YVM8
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