Research workbench
Crystal structure of the mutant P311A of enolase superfamily member from vibrionales bacterium complexed with mg and D-arabinonate
Analyse Crystal structure of the mutant P311A of enolase superfamily member from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SBF
- Type
- protein
- Length
- 1,583 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate racemase / muconate lactonizing enzyme
- UniProt
- A5KUH4
- Ligands
- D8T, MG
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Mandelate racemase / muconate lactonizing enzyme | protein | 397 | 41% helix, 17% strand | A5KUH4 |
| B | Mandelate racemase / muconate lactonizing enzyme | protein | 390 | 41% helix, 17% strand | A5KUH4 |
| D | Mandelate racemase / muconate lactonizing enzyme | protein | 399 | 41% helix, 17% strand | A5KUH4 |
Ligands and binding sites
- D8T · D-arabinonic acid · ligand · 4 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.88 | 0.92 | 85 | empty |
| 2 | 696 | 0.87 | 0.91 | 84 | empty |
| 3 | 61 | 0.73 | 0.99 | 19 | empty |
| 4 | 389 | 0.67 | 0.81 | 50 | empty |
| 5 | 486 | 0.66 | 0.78 | 41 | EPE, D8T |
Interfaces
5 interfaces between chains.
- B–C · 2570 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 2561 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1312 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1293 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1277 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3SBF · Crystal structure of the mutant P311A of enolase superfamily member from VIBRIONALES… · the same entry in another collection · chain A against A, TM-score 1.00
- A5KUH4 · AlphaFold monomer V2.0 prediction for D-galactonate dehydratase family member… · a predicted model of the same protein · 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 A5KUH4
- Elsewhere: RCSB PDB 3SBF · PDBe 3SBF · UniProt A5KUH4
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