Research workbench
Structure of cdps from staphylococcus haemolyticus
Analyse Structure of cdps from staphylococcus haemolyticus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EZ3
- Type
- protein
- Length
- 1,296 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CYCLO(L-leucyl-L-leucyl) synthase
- EC
- 2.3.2.22
- UniProt
- Q4L2X9
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 56% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CYCLO(L-leucyl-L-leucyl) synthase (EC 2.3.2.22) | protein | 220 | 55% helix, 15% strand | Q4L2X9 |
| B | CYCLO(L-leucyl-L-leucyl) synthase (EC 2.3.2.22) | protein | 214 | 57% helix, 16% strand | Q4L2X9 |
| C | CYCLO(L-leucyl-L-leucyl) synthase (EC 2.3.2.22) | protein | 217 | 57% helix, 15% strand | Q4L2X9 |
| D | CYCLO(L-leucyl-L-leucyl) synthase (EC 2.3.2.22) | protein | 215 | 57% helix, 14% strand | Q4L2X9 |
| E | CYCLO(L-leucyl-L-leucyl) synthase (EC 2.3.2.22) | protein | 213 | 53% helix, 15% strand | Q4L2X9 |
| F | CYCLO(L-leucyl-L-leucyl) synthase (EC 2.3.2.22) | protein | 217 | 56% helix, 16% strand | Q4L2X9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.79 | 0.85 | 66 | SO4 |
| 2 | 549 | 0.79 | 0.85 | 67 | SO4 |
| 3 | 450 | 0.78 | 0.86 | 53 | SO4 |
| 4 | 333 | 0.77 | 0.87 | 43 | SO4 |
| 5 | 926 | 0.74 | 0.78 | 65 | empty |
Interfaces
4 interfaces between chains.
- A–C · 967 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 941 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 818 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 804 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 Q4L2X9
- Elsewhere: RCSB PDB 6EZ3 · PDBe 6EZ3 · UniProt Q4L2X9
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