MolNFT v1 · #67600 · protein
The high resolution structure of gatcab
3IP4 · Glutamyl-TRNA(GLN) amidotransferase subunit a: “The high resolution structure of gatcab”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.69). MolNFT v1 #67600 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3IP4
- Type
- protein
- Length
- 1,059 residues
- Chains
- 3
- 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
- P63488, P64201, P68807
- Ligands
- MG
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamyl-TRNA(GLN) amidotransferase subunit a (EC 6.3.5.-) | protein | 485 | 42% helix, 15% strand | P63488 |
| B | ASPARTYL/GLUTAMYL-TRNA(ASN/GLN) amidotransferase subunit B (EC 6.3.5.-) | protein | 482 | 40% helix, 21% strand | P64201 |
| C | ASPARTYL/GLUTAMYL-TRNA(ASN/GLN) amidotransferase subunit C (EC 6.3.5.-) | protein | 92 | 41% helix, 9% strand | P68807 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.69 | 0.75 | 73 | empty |
| 2 | 85 | 0.61 | 0.88 | 12 | empty |
| 3 | 364 | 0.59 | 0.76 | 30 | empty |
| 4 | 89 | 0.54 | 0.85 | 31 | empty |
| 5 | 72 | 0.43 | 0.81 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2473 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1880 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1412 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3IP4 · The high resolution structure of GatCAB · the same entry in another collection · chain A against A, TM-score 1.00
- P63488 · AlphaFold monomer V2.0 prediction for glutamyl-TRNA(GLN) amidotransferase subunit a… · a predicted model of the same protein · chain A against A, TM-score 1.00
- P68807 · AlphaFold monomer V2.0 prediction for ASPARTYL/GLUTAMYL-TRNA(ASN/GLN) amidotransferase… · a predicted model of the same protein · chain C against A, TM-score 0.92
- P64201 · AlphaFold monomer V2.0 prediction for ASPARTYL/GLUTAMYL-TRNA(ASN/GLN) amidotransferase… · a predicted model of the same protein · chain B against A, TM-score 0.87
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 P63488
- Every structure of UniProt P64201
- Every structure of UniProt P68807
- Elsewhere: RCSB PDB 3IP4 · PDBe 3IP4 · UniProt P63488 · UniProt P64201 · UniProt P68807
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