MolNFT v1 · #75489 · protein
Crystal structure of phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod 1 (fragment 14-158) from synechocystis sp. pcc 6803, northeast structural genomics consortium target SGR182A
3PRU · Phycobilisome 32.1 kda linker polypeptide, phycocyanin…: “Crystal structure of phycobilisome 32.1 kda linker polypeptide, phycocyanin-associated, rod 1 (fragment…”. X-ray diffraction, 2 ligands (NA, CL), 5 pockets (best druggability…
- PDB
- 3PRU
- Type
- protein
- Length
- 558 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycobilisome 32.1 kda linker polypeptide, phycocyanin- associated, rod 1
- UniProt
- P73203
- Ligands
- NA, CL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Phycobilisome 32.1 kda linker polypeptide, phycocyanin- associated, rod 1 | protein | 137 | 63% helix, 1% strand | P73203 |
| A | Phycobilisome 32.1 kda linker polypeptide, phycocyanin- associated, rod 1 | protein | 142 | 61% helix, 1% strand | P73203 |
| B | Phycobilisome 32.1 kda linker polypeptide, phycocyanin- associated, rod 1 | protein | 144 | 62% helix, 1% strand | P73203 |
| D | Phycobilisome 32.1 kda linker polypeptide, phycocyanin- associated, rod 1 | protein | 135 | 65% helix, 1% strand | P73203 |
Ligands and binding sites
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 | 66 | 0.72 | 0.97 | 19 | empty |
| 2 | 631 | 0.72 | 0.79 | 66 | empty |
| 3 | 288 | 0.56 | 0.76 | 35 | CL |
| 4 | 117 | 0.41 | 0.76 | 19 | empty |
| 5 | 130 | 0.40 | 0.75 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1269 Ų buried · 17 hydrogen bonds · protein-protein
- C–A · 517 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 503 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 374 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3PRU · Crystal Structure of Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated… · the same entry in another collection · chain C against C, TM-score 1.00
- P73203 · AlphaFold monomer V2.0 prediction for phycobilisome 32.1 kda linker polypeptide… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P73203
- Elsewhere: RCSB PDB 3PRU · PDBe 3PRU · UniProt P73203
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