MolNFT v1 · #98883 · protein
Light harvesting complex PE555 from the cryptophyte hemiselmis andersenii CCMP644
4LMX · Cryptophyte phycoerythrin (alpha-2 chain): “Light harvesting complex PE555 from the cryptophyte hemiselmis andersenii CCMP644”. X-ray diffraction, 2 ligands (PEB, DBV), 20 pockets (best druggability 0.84). MolNFT v1 #98883 on…
- PDB
- 4LMX
- Type
- protein
- Length
- 1,445 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cryptophyte phycoerythrin (alpha-2 chain); Cryptophyte phycoerythrin (beta chain)…
- Ligands
- PEB, DBV
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cryptophyte phycoerythrin (alpha-2 chain) | protein | 62 | 16% helix, 29% strand | — |
| B | Cryptophyte phycoerythrin (beta chain) | protein | 177 | 71% helix, 2% strand | — |
| C | Cryptophyte phycoerythrin (alpha-1 chain) | protein | 66 | 15% helix, 27% strand | — |
| D, J, L | Cryptophyte phycoerythrin (beta chain) | protein | 175 | 71% helix, 2% strand | — |
| E, I, K | Cryptophyte phycoerythrin (alpha-1/ALPHA-2 chain) | protein | 66 | 15% helix, 27% strand | — |
| F, H | Cryptophyte phycoerythrin (beta chain) | protein | 176 | 70% helix, 2% strand | — |
| G | Cryptophyte phycoerythrin (alpha-1/ALPHA-2 chain) | protein | 65 | 15% helix, 28% strand | — |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 18 copies · chains A, B, C, D, H, E, F, G, I, J, K, L
- DBV · 15,16-dihydrobiliverdin · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.84 | 0.86 | 90 | PEB |
| 2 | 1072 | 0.84 | 0.85 | 103 | DBV |
| 3 | 1144 | 0.80 | 0.81 | 109 | PEB, DBV |
| 4 | 926 | 0.80 | 0.82 | 75 | DBV |
| 5 | 193 | 0.72 | 0.89 | 35 | PEB |
Interfaces
28 interfaces between chains.
- E–F · 2071 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 2052 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2046 Ų buried · 14 hydrogen bonds · protein-protein
- K–L · 2008 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 2005 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 cofactor, 12 covalent, 6 modified (phycoerythrobilin attachment, covalent ligand, hydroxylation).
Compared structures
- 4LMX · Light harvesting complex PE555 from the cryptophyte Hemiselmis andersenii CCMP644 · the same entry in another collection · chain D against D, 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 4LMX · PDBe 4LMX
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.