MolNFT v1 · #95340 · protein
(M)L214N mutant of the rhodobacter sphaeroides reaction center
4IN7 · Reaction center protein H chain: “(M)L214N mutant of the rhodobacter sphaeroides reaction center”. X-ray diffraction, 12 ligands (BCL, U10, HTO), 13 pockets (best druggability 0.82). MolNFT v1 #95340 on GenesisL1: 3D structure…
- PDB
- 4IN7
- 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
- BCL, U10, HTO, BPH, GGD, SPO, CDL, PC1, K, FE, MG, PO4
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 52% 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 | 64% helix, 4% strand | P0C0Y8 |
| M | Reaction center protein M chain | protein | 302 | 63% helix, 4% strand | P0C0Y9 |
Ligands and binding sites
- BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
- U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M
- HTO · Heptane-1,2,3-triol · ligand · 2 copies · chains L
- BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
- 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
- K · Potassium ion · metal · chains H
- FE · Fe (III) ion · metal · chains L, M
- MG · Magnesium ion · metal · chains 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, H, M
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 | 1162 | 0.82 | 0.82 | 91 | BCL, MG |
| 2 | 114 | 0.78 | 0.97 | 32 | empty |
| 3 | 215 | 0.68 | 0.85 | 29 | U10 |
| 4 | 220 | 0.63 | 0.83 | 39 | empty |
| 5 | 141 | 0.59 | 0.83 | 24 | U10 |
Interfaces
3 interfaces between chains.
- L–M · 4545 Ų buried · 68 hydrogen bonds · protein-protein
- H–M · 2798 Ų buried · 38 hydrogen bonds · protein-protein
- H–L · 1570 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4IN7 · (M)L214N mutant of the Rhodobacter sphaeroides Reaction Center · 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 4IN7 · PDBe 4IN7 · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9
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