MolNFT v1 · #178212 · protein
Crystal structure of phycoerythrin from halomicronema sp. R31DM
7F86 · Phycoerythrin beta subunit: “Crystal structure of phycoerythrin from halomicronema sp. R31DM”. X-ray diffraction, 1 ligand (PEB), 20 pockets (best druggability 0.89). MolNFT v1 #178212 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7F86
- Type
- protein
- Length
- 4,176 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycoerythrin beta subunit; Phycoerythrin alpha subunit
- Ligands
- PEB
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M, C, E, G, I, K, N, P, R, T, V, X | Phycoerythrin beta subunit | protein | 184 | 72% helix, 0% strand | — |
| A, D, B, F, H, J, L, O, Q, U, W, Y | Phycoerythrin alpha subunit | protein | 164 | 77% helix, 0% strand | — |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 60 copies · chains M, A, W, N, D, B, F, C, H, J, P, L, G, O, V, Q, U, K, I, E, R, Y, T, X
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 | 1059 | 0.89 | 0.91 | 141 | PEB |
| 2 | 1002 | 0.89 | 0.90 | 128 | PEB |
| 3 | 1058 | 0.89 | 0.90 | 137 | PEB |
| 4 | 553 | 0.85 | 0.90 | 86 | PEB |
| 5 | 238 | 0.81 | 0.93 | 39 | PEB |
Interfaces
57 interfaces between chains.
- U–V · 1522 Ų buried · 15 hydrogen bonds · protein-protein
- H–I · 1518 Ų buried · 15 hydrogen bonds · protein-protein
- Q–R · 1500 Ų buried · 15 hydrogen bonds · protein-protein
- M–A · 1499 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1495 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 cofactor, 12 modified (phycoerythrobilin attachment, nonstandard).
Compared structures
- 7F86 · Crystal structure of Phycoerythrin from Halomicronema Sp. R31DM · the same entry in another collection · chain M against M, 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
- Elsewhere: RCSB PDB 7F86 · PDBe 7F86
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