MolNFT v1 · #32829 · protein
Specificity of the trypanothione-dependednt leishmania major glyoxalase I: structure and biochemical comparison with the human enzyme
2C21 · Trypanothione-dependent glyoxalase I: “Specificity of the trypanothione-dependednt leishmania major glyoxalase I: structure and biochemical…”. X-ray diffraction, 2 ligands (NI, NA), 12 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 2C21
- Type
- protein
- Length
- 834 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypanothione-dependent glyoxalase I
- EC
- 4.1.1.-
- UniProt
- Q68RJ8
- Ligands
- NI, NA
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Trypanothione-dependent glyoxalase I (EC 4.1.1.-) | protein | 139 | 28% helix, 38% strand | Q68RJ8 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 2 copies · chains B, C, D, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, B, C, D, E, F
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.72 | 0.80 | 52 | empty |
| 2 | 561 | 0.72 | 0.80 | 48 | empty |
| 3 | 421 | 0.67 | 0.79 | 75 | MPD |
| 4 | 172 | 0.52 | 0.78 | 23 | empty |
| 5 | 197 | 0.51 | 0.76 | 24 | MPD, MRD |
Interfaces
8 interfaces between chains.
- E–F · 2625 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2583 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2549 Ų buried · 46 hydrogen bonds · protein-protein
- D–E · 559 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 528 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2C21 · Specificity of the Trypanothione-dependednt Leishmania major Glyoxalase I: Structure and… · the same entry in another collection · chain F against F, 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 Q68RJ8
- Elsewhere: RCSB PDB 2C21 · PDBe 2C21 · UniProt Q68RJ8
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