Research workbench
Crystal structure of (S)-ureidoglycine aminohydrolase from arabidopsis thaliana in complex with its substrate, (S)-ureidoglycine
Analyse Crystal structure of (S)-ureidoglycine aminohydrolase from arabidopsis thaliana… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E2S
- Type
- protein
- Length
- 4,128 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ureidoglycine aminohydrolase
- EC
- 3.5.3.-
- UniProt
- Q8GXV5
- Ligands
- UGY, MN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Ureidoglycine aminohydrolase (EC 3.5.3.-) | protein | 258 | 6% helix, 47% strand | Q8GXV5 |
Ligands and binding sites
- UGY · (2S)-amino(carbamoylamino)ethanoic acid · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- MN · Manganese (II) ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
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 | 986 | 0.80 | 0.81 | 61 | empty |
| 2 | 560 | 0.78 | 0.85 | 62 | UGY |
| 3 | 647 | 0.78 | 0.83 | 73 | UGY |
| 4 | 647 | 0.75 | 0.81 | 84 | UGY |
| 5 | 700 | 0.75 | 0.80 | 80 | UGY |
Interfaces
35 interfaces between chains.
- A–D · 1149 Ų buried · 9 hydrogen bonds · protein-protein
- G–I · 1101 Ų buried · 7 hydrogen bonds · protein-protein
- F–L · 1099 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1092 Ų buried · 7 hydrogen bonds · protein-protein
- C–G · 1085 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4E2S · Crystal structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana in… · the same entry in another collection · chain I against I, 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 Q8GXV5
- Elsewhere: RCSB PDB 4E2S · PDBe 4E2S · UniProt Q8GXV5
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