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Crystal structure of DOC2B C2A domain
Analyse Crystal structure of DOC2B C2A domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LCV
- Type
- protein
- Length
- 509 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double C2-like domain-containing protein beta
- UniProt
- P70610
- Ligands
- CA, SO4
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double C2-like domain-containing protein beta | protein | 123 | 12% helix, 51% strand | P70610 |
| B | Double C2-like domain-containing protein beta | protein | 131 | 9% helix, 47% strand | P70610 |
| C | Double C2-like domain-containing protein beta | protein | 129 | 12% helix, 50% strand | P70610 |
| D | Double C2-like domain-containing protein beta | protein | 126 | 8% helix, 50% strand | P70610 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · chains A
- FLC · Citrate anion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.65 | 0.75 | 56 | empty |
| 2 | 549 | 0.64 | 0.76 | 51 | empty |
| 3 | 67 | 0.30 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 430 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 370 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 110 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 61 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
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 P70610
- Elsewhere: RCSB PDB 4LCV · PDBe 4LCV · UniProt P70610
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