Research workbench
Crystal structure of CMIS2 with inhibitor
Analyse Crystal structure of CMIS2 with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J39
- Type
- protein
- Length
- 726 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-dependent glycine oxydase
- UniProt
- X5IYZ1
- Ligands
- FAD, B6X
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD-dependent glycine oxydase | protein | 368 | 36% helix, 27% strand | X5IYZ1 |
| B | FAD-dependent glycine oxydase | protein | 358 | 36% helix, 27% strand | X5IYZ1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- B6X · (3R)-3-[(carboxymethyl)sulfanyl]nonanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.82 | 0.88 | 84 | FAD, B6X |
| 2 | 626 | 0.81 | 0.86 | 81 | FAD, B6X |
| 3 | 633 | 0.75 | 0.81 | 40 | empty |
| 4 | 60 | 0.38 | 0.80 | 14 | empty |
| 5 | 72 | 0.29 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 402 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6J39 · Crystal structure of CmiS2 with inhibitor · 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 X5IYZ1
- Elsewhere: RCSB PDB 6J39 · PDBe 6J39 · UniProt X5IYZ1
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