Research workbench
Structure of cdps from nocardia brasiliensis
Analyse Structure of cdps from nocardia brasiliensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MLQ
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cdps
- UniProt
- K0F6G5
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cdps | protein | 226 | 55% helix, 16% strand | K0F6G5 |
Ligands and binding sites
- CIT · Citric acid · additive · 3 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.80 | 0.97 | 23 | empty |
| 2 | 509 | 0.65 | 0.77 | 40 | empty |
| 3 | 343 | 0.61 | 0.78 | 43 | empty |
| 4 | 270 | 0.56 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 719 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 5MLQ · Structure of CDPS from Nocardia brasiliensis · 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 K0F6G5
- Elsewhere: RCSB PDB 5MLQ · PDBe 5MLQ · UniProt K0F6G5
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