Research workbench
Crystal structure of mccd protein
Analyse Crystal structure of mccd protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FCD
- Type
- protein
- Length
- 467 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unk-unk-unk-mse-unk; Unk-unk-unk-unk-mse-unk; Mccd
- UniProt
- Q83Y56
- Ligands
- CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Unk-unk-unk-mse-unk | protein | 5 | 0% helix, 0% strand | — |
| E | Unk-unk-unk-unk-mse-unk | protein | 6 | 0% helix, 0% strand | — |
| A | Mccd | protein | 228 | 45% helix, 26% strand | Q83Y56 |
| B | Mccd | protein | 228 | 46% helix, 25% strand | Q83Y56 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.70 | 0.77 | 94 | empty |
| 2 | 154 | 0.51 | 0.79 | 29 | empty |
| 3 | 116 | 0.50 | 0.81 | 27 | empty |
| 4 | 100 | 0.36 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 406 Ų buried · 7 hydrogen bonds · protein-protein
- E–B · 291 Ų buried · 1 hydrogen bond · protein-protein
- D–A · 235 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5FCD · Crystal structure of MccD protein · 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 Q83Y56
- Elsewhere: RCSB PDB 5FCD · PDBe 5FCD · UniProt Q83Y56
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