Research workbench
Crystal structure of enolase TBIS_1083(TARGET efi-502310) from thermobispora bispora dsm 43833, an open loop conformation
Analyse Crystal structure of enolase TBIS_1083(TARGET efi-502310) from thermobispora… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DHG
- Type
- protein
- Length
- 1,699 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mandelate RACEMASE/MUCONATE lactonizing protein
- UniProt
- D6Y7Y6
- Ligands
- UNL, IOD, PO4
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 428 | 38% helix, 19% strand | D6Y7Y6 |
| B | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 420 | 38% helix, 19% strand | D6Y7Y6 |
| C | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 424 | 38% helix, 19% strand | D6Y7Y6 |
| D | Mandelate RACEMASE/MUCONATE lactonizing protein | protein | 427 | 38% helix, 19% strand | D6Y7Y6 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · chains B
- IOD · Iodide ion · ion · 11 copies · chains A, D, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.87 | 0.88 | 132 | PO4, GOL, IOD |
| 2 | 915 | 0.81 | 0.83 | 84 | empty |
| 3 | 163 | 0.79 | 0.95 | 34 | empty |
| 4 | 87 | 0.75 | 0.97 | 20 | empty |
| 5 | 446 | 0.66 | 0.79 | 44 | PO4 |
Interfaces
4 interfaces between chains.
- A–C · 1376 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1327 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 808 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 320 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4DHG · Crystal structure of enolase TBIS_1083(TARGET EFI-502310) from Thermobispora bispora dsm… · 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 D6Y7Y6
- Elsewhere: RCSB PDB 4DHG · PDBe 4DHG · UniProt D6Y7Y6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.