Research workbench
Crystal structure of aminotransferase crmg from actinoalloteichus sp. WH1-2216-6 in complex with amino donor L-gln
Analyse Crystal structure of aminotransferase crmg from actinoalloteichus sp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JC9
- Type
- protein
- Length
- 2,044 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crmg
- UniProt
- H8Y6N2
- Ligands
- PLP, GLN
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Crmg | protein | 512 | 46% helix, 19% strand | H8Y6N2 |
| D | Crmg | protein | 508 | 46% helix, 19% strand | H8Y6N2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- GLN · Glutamine · ligand · chains C, D
- ACY · Acetic acid · additive · chains B
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.84 | 0.89 | 69 | PLP |
| 2 | 627 | 0.83 | 0.88 | 79 | PLP |
| 3 | 607 | 0.83 | 0.88 | 73 | PLP |
| 4 | 595 | 0.83 | 0.88 | 76 | GLN, PLP |
| 5 | 947 | 0.81 | 0.83 | 102 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4758 Ų buried · 73 hydrogen bonds · protein-protein
- C–D · 4746 Ų buried · 70 hydrogen bonds · protein-protein
- A–C · 998 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 164 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 163 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6JC9 · Crystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in… · 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 H8Y6N2
- Elsewhere: RCSB PDB 6JC9 · PDBe 6JC9 · UniProt H8Y6N2
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