MolNFT v1 · #51952 · protein
The monoclinic structure of phycocyanin from gloeobacter violaceus
2VML · Phycocyanin alpha chain: “The monoclinic structure of phycocyanin from gloeobacter violaceus”. X-ray diffraction, 1 ligand (CYC), 20 pockets (best druggability 0.83). MolNFT v1 #51952 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VML
- Type
- protein
- Length
- 2,004 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycocyanin alpha chain; Phycocyanin beta chain
- UniProt
- Q7M7F7, Q7M7C7
- Ligands
- CYC
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Phycocyanin alpha chain | protein | 162 | 80% helix, 0% strand | Q7M7F7 |
| B, D, F, H, J, L | Phycocyanin beta chain | protein | 172 | 77% helix, 0% strand | Q7M7C7 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 18 copies · chains A, F, B, K, C, D, G, E, I, J, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.83 | 0.84 | 110 | empty |
| 2 | 1199 | 0.82 | 0.83 | 129 | empty |
| 3 | 1175 | 0.82 | 0.83 | 118 | empty |
| 4 | 322 | 0.79 | 0.89 | 34 | CYC |
| 5 | 322 | 0.79 | 0.89 | 37 | CYC |
Interfaces
30 interfaces between chains.
- C–D · 1619 Ų buried · 14 hydrogen bonds · protein-protein
- K–L · 1583 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1565 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 1562 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1560 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 cofactor (phycocyanobilin attachment).
Compared structures
- 2VML · The monoclinic structure of phycocyanin from Gloeobacter violaceus · the same entry in another collection · chain G against G, 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 Q7M7F7
- Every structure of UniProt Q7M7C7
- Elsewhere: RCSB PDB 2VML · PDBe 2VML · UniProt Q7M7F7 · UniProt Q7M7C7
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