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Structure of a quintuple mutant of photosynthetic reaction center from rhodobacter sphaeroides

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PDB: 1YF6
Type: protein
Length: 820 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reaction center protein L chain; Reaction center protein M chain; Reaction center protein…
UniProt: P02954, P02953, P11846
Ligands: BCL, U10, BPH, HTO, SPO, CDL, FE2, PO4, CL
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Reaction center protein L chain	protein	281	62% helix, 4% strand	P02954
M	Reaction center protein M chain	protein	301	64% helix, 4% strand	P02953
H	Reaction center protein H chain	protein	238	26% helix, 24% strand	P11846

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 5 copies · chains L, M
U10 · Ubiquinone-10 · ligand · 3 copies · chains L, M, H
BPH · Bacteriopheophytin A · ligand · chains L, M
HTO · Heptane-1,2,3-triol · ligand · chains L
SPO · Spheroidene · ligand · chains M
CDL · Cardiolipin · ligand · chains L, M, H
FE2 · Fe (II) ion · metal · chains L, M
PO4 · Phosphate ion · ion · 2 copies · chains M, H
CL · Chloride ion · ion · chains M
LDA · Lauryl dimethylamine-N-oxide · additive · 3 copies · chains L, M, H
GOL · Glycerol · additive · chains L, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.83	0.84	89	BCL, BPH
2	130	0.79	0.97	33	empty
3	60	0.69	0.96	14	empty
4	150	0.63	0.85	29	U10
5	92	0.57	0.86	17	empty

Interfaces

3 interfaces between chains.

L–M · 4498 Å² buried · 68 hydrogen bonds · protein-protein
M–H · 2920 Å² buried · 41 hydrogen bonds · protein-protein
L–H · 1596 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1YF6 · Structure of a quintuple mutant of photosynthetic reaction center from rhodobacter… · the same entry in another collection · chain L against L, TM-score 1.00

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Elsewhere: RCSB PDB 1YF6 · PDBe 1YF6 · UniProt P02954 · UniProt P02953 · UniProt P11846

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