Research workbench
X-ray structure of neob from streptomyces fradiae in complex with neamine as an external aldimine
Analyse X-ray structure of neob from streptomyces fradiae in complex with neamine as an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CBL
- Type
- protein
- Length
- 3,272 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neamine transaminase neon
- EC
- 2.6.1.93, 2.6.1.95
- UniProt
- Q53U08
- Ligands
- DOW, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Neamine transaminase neon (EC 2.6.1.93, 2.6.1.95) | protein | 409 | 41% helix, 16% strand | Q53U08 |
Ligands and binding sites
- DOW · (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2-amino-2,6-dideoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-alpha-D-glucopyranoside · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.78 | 0.82 | 84 | DOW |
| 2 | 735 | 0.77 | 0.82 | 82 | DOW |
| 3 | 763 | 0.77 | 0.81 | 86 | DOW |
| 4 | 752 | 0.77 | 0.81 | 83 | DOW |
| 5 | 751 | 0.77 | 0.81 | 81 | DOW |
Interfaces
12 interfaces between chains.
- E–F · 3437 Ų buried · 58 hydrogen bonds · protein-protein
- G–H · 3420 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 3406 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 3369 Ų buried · 57 hydrogen bonds · protein-protein
- C–F · 435 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6CBL · x-ray structure of NeoB from Streptomyces fradiae in complex with neamine as an external… · the same entry in another collection · chain H against H, TM-score 1.00
- Q53U08 · AlphaFold monomer V2.0 prediction for neamine transaminase neon (Q53U08) · a predicted model of the same protein · 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 Q53U08
- Elsewhere: RCSB PDB 6CBL · PDBe 6CBL · UniProt Q53U08
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