Research workbench
Biochemical and structural characterization of a ureidoglycine aminotransferase in the klebsiella pneumoniae uric acid catabolic pathway
Analyse Biochemical and structural characterization of a ureidoglycine aminotransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NNK
- Type
- protein
- Length
- 6,560 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ureidoglycine-glyoxylate aminotransferase
- UniProt
- B5B0L4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ureidoglycine-glyoxylate aminotransferase | protein | 411 | 43% helix, 15% strand | B5B0L4 |
| B, C, D, E, F, G, H, J, K, M, O, P, R, S | Ureidoglycine-glyoxylate aminotransferase | protein | 410 | 43% helix, 15% strand | B5B0L4 |
| L | Ureidoglycine-glyoxylate aminotransferase | protein | 409 | 42% helix, 14% strand | B5B0L4 |
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 | 453 | 0.87 | 0.94 | 47 | empty |
| 2 | 496 | 0.86 | 0.93 | 48 | empty |
| 3 | 477 | 0.86 | 0.93 | 49 | empty |
| 4 | 430 | 0.86 | 0.94 | 48 | empty |
| 5 | 401 | 0.85 | 0.94 | 48 | empty |
Interfaces
30 interfaces between chains.
- A–B · 3655 Ų buried · 53 hydrogen bonds · protein-protein
- L–M · 3646 Ų buried · 53 hydrogen bonds · protein-protein
- G–H · 3621 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3616 Ų buried · 62 hydrogen bonds · protein-protein
- R–S · 3615 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (cofactor).
Compared structures
- 3NNK · Biochemical and Structural Characterization of a Ureidoglycine Aminotransferase in the… · 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 B5B0L4
- Elsewhere: RCSB PDB 3NNK · PDBe 3NNK · UniProt B5B0L4
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