Research workbench
Structure of mcbb in complex with tryptophan
Analyse Structure of mcbb in complex with tryptophan in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3X27
- Type
- protein
- Length
- 1,241 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cucumopine synthase
- UniProt
- R4QPW9
- Ligands
- TRP
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cucumopine synthase | protein | 309 | 52% helix, 18% strand | R4QPW9 |
| D | Cucumopine synthase | protein | 314 | 52% helix, 20% strand | R4QPW9 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.81 | 0.89 | 50 | TRP |
| 2 | 415 | 0.81 | 0.89 | 50 | TRP |
| 3 | 419 | 0.81 | 0.89 | 47 | TRP |
| 4 | 429 | 0.80 | 0.88 | 47 | TRP |
| 5 | 81 | 0.43 | 0.80 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3324 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 3280 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 173 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 168 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 133 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3X27 · Structure of McbB in complex with tryptophan · the same entry in another collection · chain D against D, 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 R4QPW9
- Elsewhere: RCSB PDB 3X27 · PDBe 3X27 · UniProt R4QPW9
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