Research workbench
Structure of tRNA-dependent amidotransferase gatcab from aquifex aeolicus
Analyse Structure of tRNA-dependent amidotransferase gatcab from aquifex aeolicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H0L
- Type
- protein
- Length
- 7,832 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamyl-TRNA(GLN) amidotransferase subunit a; ASPARTYL/GLUTAMYL-TRNA(ASN/GLN)…
- EC
- 6.3.5.-
- UniProt
- O66610, O66766, O67904
- Ligands
- ADP, ASN, MG, ZN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P, S, V | Glutamyl-TRNA(GLN) amidotransferase subunit a (EC 6.3.5.-) | protein | 478 | 42% helix, 14% strand | O66610 |
| B, E, H, K, N, Q, T, W | ASPARTYL/GLUTAMYL-TRNA(ASN/GLN) amidotransferase subunit B (EC 6.3.5.-) | protein | 410 | 37% helix, 23% strand | O66766 |
| C, F, I, L, O, R, U, X | Glutamyl-TRNA(GLN) amidotransferase subunit C (EC 6.3.5.-) | protein | 91 | 38% helix, 9% strand | O67904 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains B, E, H, K, N, Q, T, W
- ASN · Asparagine · ligand · 8 copies · chains A, D, G, J, M, P, S, V
- MG · Magnesium ion · metal · 8 copies · chains B, E, H, K, N, Q, T, W
- ZN · Zinc ion · metal · 8 copies · chains B, E, H, K, N, Q, T, W
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 | 1131 | 0.80 | 0.81 | 96 | empty |
| 2 | 992 | 0.80 | 0.81 | 92 | empty |
| 3 | 736 | 0.77 | 0.81 | 67 | empty |
| 4 | 456 | 0.75 | 0.84 | 54 | empty |
| 5 | 378 | 0.75 | 0.85 | 37 | empty |
Interfaces
46 interfaces between chains.
- G–I · 2628 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 2599 Ų buried · 27 hydrogen bonds · protein-protein
- P–R · 2598 Ų buried · 19 hydrogen bonds · protein-protein
- V–X · 2590 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 2585 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 3H0L · Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus · the same entry in another collection · chain J against J, 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 O66610
- Every structure of UniProt O66766
- Every structure of UniProt O67904
- Elsewhere: RCSB PDB 3H0L · PDBe 3H0L · UniProt O66610 · UniProt O66766 · UniProt O67904
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