MolNFT v1 · #37909 · protein
Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme from bacillus subtilis complexed with mg++ at 1.8 a
2GGE · Yitf: “Crystal structure of mandelate RACEMASE/MUCONATE lactonizing enzyme from bacillus subtilis complexed with…”. X-ray diffraction, 2 ligands (MG, CL), 20 pockets (best druggability 0.86). MolNFT v1 #37909 on GenesisL1: 3D…
- PDB
- 2GGE
- Type
- protein
- Length
- 2,991 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yitf
- UniProt
- O06741
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Yitf | protein | 373 | 38% helix, 23% strand | O06741 |
| B, C, G, H | Yitf | protein | 374 | 38% helix, 23% strand | O06741 |
| D | Yitf | protein | 376 | 38% helix, 23% strand | O06741 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 3 copies · chains D, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.86 | 0.90 | 102 | empty |
| 2 | 709 | 0.86 | 0.90 | 96 | empty |
| 3 | 905 | 0.86 | 0.88 | 107 | empty |
| 4 | 923 | 0.84 | 0.85 | 120 | empty |
| 5 | 497 | 0.84 | 0.90 | 65 | empty |
Interfaces
16 interfaces between chains.
- C–D · 1234 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 1230 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1220 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1206 Ų buried · 13 hydrogen bonds · protein-protein
- E–H · 900 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2GGE · Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme from Bacillus… · the same entry in another collection · chain H against H, TM-score 1.00
- O06741 · AlphaFold monomer V2.0 prediction for putative isomerase yitf (O06741) · 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 O06741
- Elsewhere: RCSB PDB 2GGE · PDBe 2GGE · UniProt O06741
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