Research workbench
Crystal structure of aminotransferase crmg from actinoalloteichus sp. WH1-2216-6 in complex with pmp
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
- 5DDU
- Type
- protein
- Length
- 2,049 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crmg
- UniProt
- H8Y6N2
- Ligands
- PMP
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Crmg | protein | 513 | 47% helix, 19% strand | H8Y6N2 |
| B | Crmg | protein | 512 | 47% helix, 19% strand | H8Y6N2 |
| C | Crmg | protein | 511 | 47% helix, 20% strand | H8Y6N2 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · chains A, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.86 | 0.93 | 68 | PMP |
| 2 | 472 | 0.86 | 0.92 | 65 | PMP |
| 3 | 624 | 0.85 | 0.89 | 71 | PMP |
| 4 | 674 | 0.84 | 0.88 | 83 | PMP |
| 5 | 60 | 0.56 | 0.89 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4725 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 4692 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 821 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 31 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DDU · 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 5DDU · PDBe 5DDU · UniProt H8Y6N2
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