MolNFT v1 · #126481 · protein
Alpha-amino epsilon-caprolactam racemase D210A mutant in complex with plp and geminal diamine intermediate
5M4B · Aminotransferase class-III: “Alpha-amino epsilon-caprolactam racemase D210A mutant in complex with plp and geminal diamine intermediate”. X-ray diffraction, 1 ligand (7F7), 3 pockets (best druggability 0.62). MolNFT v1 #126481 on…
- PDB
- 5M4B
- Type
- protein
- Length
- 439 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase class-III
- EC
- 5.1.1.15
- UniProt
- N6UXY4
- Ligands
- 7F7
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase class-III (EC 5.1.1.15) | protein | 439 | 40% helix, 18% strand | N6UXY4 |
Ligands and binding sites
- 7F7 · [6-methyl-5-oxidanyl-4-[(~{E})-[(3~{R})-2-oxidanylideneazepan-3-yl]iminomethyl]pyridin-3-yl]methyl dihydrogen phosphate · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.62 | 0.77 | 48 | 7F7 |
| 2 | 210 | 0.56 | 0.79 | 26 | empty |
| 3 | 103 | 0.45 | 0.79 | 20 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5M4B · Alpha-amino epsilon-caprolactam racemase D210A mutant in complex with PLP and geminal… · 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 N6UXY4
- Elsewhere: RCSB PDB 5M4B · PDBe 5M4B · UniProt N6UXY4
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