Research workbench
Zinc substituted reaction center M(L214H) variant of rhodobacter sphaeroides
Analyse Zinc substituted reaction center M(L214H) variant of rhodobacter sphaeroides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N7L
- Type
- protein
- Length
- 823 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reaction center protein H chain; Reaction center protein L chain; Reaction center protein…
- UniProt
- P0C0Y7, P0C0Y8, P0C0Y9
- Ligands
- 2GO, U10, HTO, GGD, SPO, CDL, PC1, FE, PO4
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Reaction center protein H chain | protein | 240 | 23% helix, 25% strand | P0C0Y7 |
| L | Reaction center protein L chain | protein | 281 | 62% helix, 3% strand | P0C0Y8 |
| M | Reaction center protein M chain | protein | 302 | 64% helix, 4% strand | P0C0Y9 |
Ligands and binding sites
- 2GO · [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]zinc · ligand · 6 copies · chains L, M
- U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M
- HTO · Heptane-1,2,3-triol · ligand · 2 copies · chains L
- GGD · Nonadec-10-enoic acid 2-[3,4-dihydroxy-6-hydroxymethyl-5-(3,4,5-trihydroxy-6-hydroxymethyl-tetrahydro-pyran-2-yloxy)-tetrahydro-pyran-2-yloxy] -1-octadec-9-enoyloxymethyl-ethyl ester · ligand · chains H, L, M
- SPO · Spheroidene · ligand · chains M
- CDL · Cardiolipin · ligand · chains H, L, M
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · chains L, M
- FE · Fe (III) ion · metal · chains L, M
- PO4 · Phosphate ion · ion · chains L
- GOL · Glycerol · additive · 7 copies · chains H, L, M
- LDA · Lauryl dimethylamine-N-oxide · additive · 5 copies · chains L, M, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.82 | 0.84 | 69 | 2GO |
| 2 | 115 | 0.78 | 0.97 | 34 | empty |
| 3 | 129 | 0.70 | 0.90 | 19 | U10 |
| 4 | 211 | 0.63 | 0.83 | 39 | empty |
| 5 | 129 | 0.59 | 0.84 | 19 | SPO |
Interfaces
3 interfaces between chains.
- L–M · 4585 Ų buried · 68 hydrogen bonds · protein-protein
- H–M · 2786 Ų buried · 42 hydrogen bonds · protein-protein
- H–L · 1590 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4N7L · Zinc Substituted Reaction Center M(L214H) Variant of Rhodobacter sphaeroides · the same entry in another collection · chain H against H, 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 P0C0Y7
- Every structure of UniProt P0C0Y8
- Every structure of UniProt P0C0Y9
- Elsewhere: RCSB PDB 4N7L · PDBe 4N7L · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9
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