MolNFT v1 · #116448 · protein
Crystal structure of aminotransferase crmg from actinoalloteichus sp. WH1-2216-6 in complex with the pmp external aldimine adduct with caerulomycin M
5DDW: “Crystal structure of aminotransferase crmg from actinoalloteichus sp. WH1-2216-6 in complex with the pmp…”. X-ray diffraction, 1 ligand (5B6), 17 pockets (best druggability 0.85). MolNFT v1 #116448 on GenesisL1: 3D structure…
- PDB
- 5DDW
- Type
- protein
- Length
- 2,045 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crmg
- UniProt
- H8Y6N2
- Ligands
- 5B6
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Crmg | protein | 512 | 47% helix, 19% strand | H8Y6N2 |
| B | Crmg | protein | 511 | 47% helix, 19% strand | H8Y6N2 |
| C | Crmg | protein | 511 | 47% helix, 19% strand | H8Y6N2 |
| D | Crmg | protein | 511 | 47% helix, 19% strand | H8Y6N2 |
Ligands and binding sites
- 5B6 · [5-hydroxy-4-({(E)-[(4-hydroxy-2,2'-bipyridin-6-yl) methylidene]amino}methyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.85 | 0.92 | 71 | 5B6 |
| 2 | 451 | 0.85 | 0.93 | 68 | 5B6 |
| 3 | 608 | 0.84 | 0.89 | 69 | 5B6 |
| 4 | 594 | 0.84 | 0.89 | 71 | 5B6 |
| 5 | 90 | 0.61 | 0.89 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4704 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 4678 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 817 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 31 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
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 5DDW · PDBe 5DDW · UniProt H8Y6N2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.