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Crystal structure of an enolase from pantoea ananatis (efi target efi- 501676) with bound D-gluconate and mg
Analyse Crystal structure of an enolase from pantoea ananatis (efi target efi- 501676)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T6C
- Type
- protein
- Length
- 829 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative mand family dehydratase
- EC
- 4.2.1.-
- UniProt
- D4GJ14
- Ligands
- GCO, MG, UNX, CL
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative mand family dehydratase (EC 4.2.1.-) | protein | 415 | 40% helix, 16% strand | D4GJ14 |
| B | Putative mand family dehydratase (EC 4.2.1.-) | protein | 414 | 41% helix, 17% strand | D4GJ14 |
Ligands and binding sites
- GCO · D-gluconic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.68 | 0.96 | 22 | GCO |
| 2 | 220 | 0.66 | 0.84 | 32 | EDO |
| 3 | 238 | 0.64 | 0.82 | 28 | EDO |
| 4 | 315 | 0.57 | 0.77 | 44 | GCO |
| 5 | 153 | 0.55 | 0.81 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 2667 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 3T6C · Crystal structure of an enolase from pantoea ananatis (efi target efi-501676) with bound… · the same entry in another collection · chain A against A, TM-score 1.00
- D4GJ14 · AlphaFold monomer V2.0 prediction for D-galactonate dehydratase family member rspa… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 D4GJ14
- Elsewhere: RCSB PDB 3T6C · PDBe 3T6C · UniProt D4GJ14
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