Research workbench
Crystal structure of water-soluble chlorophyll protein from lepidium virginicum at 2.00 ångström resolution
Analyse Crystal structure of water-soluble chlorophyll protein from lepidium virginicum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DRE
- Type
- protein
- Length
- 699 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Water-soluble chlorophyll protein
- UniProt
- O04797
- Ligands
- CLA
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Water-soluble chlorophyll protein | protein | 172 | 2% helix, 37% strand | O04797 |
| B | Water-soluble chlorophyll protein | protein | 173 | 2% helix, 35% strand | O04797 |
| C, D | Water-soluble chlorophyll protein | protein | 177 | 0% helix, 39% strand | O04797 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.74 | 0.83 | 40 | CLA |
| 2 | 450 | 0.74 | 0.82 | 39 | CLA |
| 3 | 263 | 0.52 | 0.75 | 39 | empty |
| 4 | 248 | 0.49 | 0.74 | 40 | empty |
| 5 | 54 | 0.30 | 0.76 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 623 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 581 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 410 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 409 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 159 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2DRE · Crystal structure of Water-soluble chlorophyll protein from lepidium virginicum at 2.00… · 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 O04797
- Elsewhere: RCSB PDB 2DRE · PDBe 2DRE · UniProt O04797
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