MolNFT v1 · #106024 · protein
Crystal structure of allophycocyanin from marine cyanobacterium phormidium sp. A09DM
4RMP: “Crystal structure of allophycocyanin from marine cyanobacterium phormidium sp. A09DM”. X-ray diffraction, 1 ligand (CYC), 3 pockets (best druggability 0.63). MolNFT v1 #106024 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4RMP
- Type
- protein
- Length
- 321 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allophycocyanin
- UniProt
- A0A078K1U6, A0A078K4M9
- Ligands
- CYC
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Allophycocyanin | protein | 160 | 81% helix, 0% strand | A0A078K1U6 |
| B | Allophycocyanin | protein | 161 | 80% helix, 0% strand | A0A078K4M9 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 2 copies · chains A, B
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 | 99 | 0.63 | 0.88 | 23 | CYC |
| 2 | 146 | 0.56 | 0.82 | 25 | CYC |
| 3 | 52 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1471 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 1 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 4RMP · Crystal structure of allophycocyanin from marine cyanobacterium Phormidium sp. A09DM · 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 A0A078K1U6
- Every structure of UniProt A0A078K4M9
- Elsewhere: RCSB PDB 4RMP · PDBe 4RMP · UniProt A0A078K1U6 · UniProt A0A078K4M9
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