MolNFT v1 · #106234 · protein
The crystal structure of a GLYOXALASE/BLEOMYCIN resistance PROTEIN/DIOXYGENASE protein from planctomyces limnophilus dsm 3776
4RT5: “The crystal structure of a GLYOXALASE/BLEOMYCIN resistance PROTEIN/DIOXYGENASE protein from planctomyces…”. X-ray diffraction, 1 ligand (NI), 3 pockets (best druggability 0.53). MolNFT v1 #106234 on GenesisL1: 3D structure, binding…
- PDB
- 4RT5
- Type
- protein
- Length
- 201 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLYOXALASE/BLEOMYCIN resistance PROTEIN/DIOXYGENASE
- EC
- 4.4.1.5
- UniProt
- D5SVJ2
- Ligands
- NI
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GLYOXALASE/BLEOMYCIN resistance PROTEIN/DIOXYGENASE (EC 4.4.1.5) | protein | 101 | 18% helix, 40% strand | D5SVJ2 |
| B | GLYOXALASE/BLEOMYCIN resistance PROTEIN/DIOXYGENASE (EC 4.4.1.5) | protein | 100 | 18% helix, 40% strand | D5SVJ2 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.53 | 0.78 | 21 | NI, TRS |
| 2 | 188 | 0.51 | 0.77 | 22 | empty |
| 3 | 102 | 0.36 | 0.74 | 19 | NI, TRS |
Interfaces
1 interface between chains.
- A–B · 1785 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 4RT5 · The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase protein… · 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 D5SVJ2
- Elsewhere: RCSB PDB 4RT5 · PDBe 4RT5 · UniProt D5SVJ2
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