MolNFT v1 · #116444 · protein
Crystal structure of aminotransferase crmg from actinoalloteichus sp. WH1-2216-6 in complex with plp
5DDS: “Crystal structure of aminotransferase crmg from actinoalloteichus sp. WH1-2216-6 in complex with plp”. X-ray diffraction, 1 ligand (PLP), 15 pockets (best druggability 0.87). MolNFT v1 #116444 on GenesisL1: 3D structure, binding…
- PDB
- 5DDS
- Type
- protein
- Length
- 2,047 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crmg
- UniProt
- H8Y6N2
- Ligands
- PLP
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Crmg | protein | 514 | 47% helix, 19% strand | H8Y6N2 |
| B | Crmg | protein | 511 | 47% helix, 19% strand | H8Y6N2 |
| C | Crmg | protein | 510 | 47% helix, 19% strand | H8Y6N2 |
| D | Crmg | protein | 512 | 47% helix, 19% strand | H8Y6N2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACY · Acetic acid · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.87 | 0.90 | 110 | PLP |
| 2 | 600 | 0.86 | 0.91 | 81 | PLP |
| 3 | 604 | 0.84 | 0.89 | 65 | PLP |
| 4 | 600 | 0.83 | 0.88 | 67 | PLP |
| 5 | 111 | 0.58 | 0.85 | 25 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4739 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 4705 Ų buried · 64 hydrogen bonds · protein-protein
- A–C · 900 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5DDS · 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 5DDS · PDBe 5DDS · UniProt H8Y6N2
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