MolNFT v1 · #58484 · protein
Crystal structure of the MN(II)-bound glyoxalase from novosphingobium aromaticivorans
3B59 · GLYOXALASE/BLEOMYCIN resistance PROTEIN/DIOXYGENASE: “Crystal structure of the MN(II)-bound glyoxalase from novosphingobium aromaticivorans”. X-ray diffraction, 1 ligand (MN), 19 pockets (best druggability 0.89). MolNFT v1 #58484 on…
- PDB
- 3B59
- Type
- protein
- Length
- 1,806 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLYOXALASE/BLEOMYCIN resistance PROTEIN/DIOXYGENASE
- UniProt
- Q2GAG3
- Ligands
- MN
- Pockets
- 19 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | GLYOXALASE/BLEOMYCIN resistance PROTEIN/DIOXYGENASE | protein | 301 | 19% helix, 35% strand | Q2GAG3 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.89 | 0.91 | 133 | empty |
| 2 | 925 | 0.88 | 0.90 | 117 | empty |
| 3 | 1115 | 0.88 | 0.89 | 136 | empty |
| 4 | 62 | 0.52 | 0.86 | 22 | empty |
| 5 | 60 | 0.51 | 0.86 | 19 | empty |
Interfaces
12 interfaces between chains.
- B–E · 715 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 705 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 688 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 677 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 672 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified (engineered).
Compared structures
- 3B59 · Crystal structure of the Mn(II)-bound glyoxalase from Novosphingobium aromaticivorans · 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 Q2GAG3
- Elsewhere: RCSB PDB 3B59 · PDBe 3B59 · UniProt Q2GAG3
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