MolNFT v1 · #153366 · protein
Crystal structure of aminotransferase crmg from actinoalloteichus sp. WH1-2216-6 in complex with amino donor L-glu
6JC8: “Crystal structure of aminotransferase crmg from actinoalloteichus sp. WH1-2216-6 in complex with amino donor…”. X-ray diffraction, 1 ligand (PL6), 17 pockets (best druggability 0.87). MolNFT v1 #153366 on GenesisL1: 3D structure…
- PDB
- 6JC8
- Type
- protein
- Length
- 2,048 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crmg
- UniProt
- H8Y6N2
- Ligands
- PL6
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Crmg | protein | 512 | 48% helix, 19% strand | H8Y6N2 |
Ligands and binding sites
- PL6 · (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-glutamic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.87 | 0.90 | 107 | PL6 |
| 2 | 723 | 0.86 | 0.90 | 102 | PL6 |
| 3 | 631 | 0.84 | 0.89 | 77 | PL6 |
| 4 | 581 | 0.84 | 0.89 | 69 | PL6 |
| 5 | 72 | 0.59 | 0.89 | 21 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4740 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 4740 Ų buried · 70 hydrogen bonds · protein-protein
- A–C · 844 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 31 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6JC8 · 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 6JC8 · PDBe 6JC8 · UniProt H8Y6N2
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