MolNFT v1 · #163434 · protein
Water-soluble chlorophyll protein (wscp) from lepidium virginicum with chlorophyll-B
6S2Y: “Water-soluble chlorophyll protein (wscp) from lepidium virginicum with chlorophyll-B”. X-ray diffraction, 1 ligand (CHL), 6 pockets (best druggability 0.77). MolNFT v1 #163434 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6S2Y
- Type
- protein
- Length
- 639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Water-soluble chlorophyll protein
- UniProt
- O04797
- Ligands
- CHL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Water-soluble chlorophyll protein | protein | 157 | 2% helix, 38% strand | O04797 |
| B | Water-soluble chlorophyll protein | protein | 159 | 2% helix, 35% strand | O04797 |
| C | Water-soluble chlorophyll protein | protein | 161 | 4% helix, 37% strand | O04797 |
| D | Water-soluble chlorophyll protein | protein | 162 | 4% helix, 38% strand | O04797 |
Ligands and binding sites
- CHL · Chlorophyll B · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.77 | 0.81 | 48 | CHL |
| 2 | 796 | 0.76 | 0.80 | 61 | CHL |
| 3 | 166 | 0.40 | 0.73 | 31 | empty |
| 4 | 164 | 0.40 | 0.72 | 30 | empty |
| 5 | 51 | 0.33 | 0.78 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 608 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 576 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 410 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 403 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 158 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6S2Y · Water-soluble Chlorophyll Protein (WSCP) from Lepidium virginicum with Chlorophyll-b · 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 6S2Y · PDBe 6S2Y · UniProt O04797
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