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Structure of photosynthetic reaction center with bacteriochlorophyll- bacteriopheophytin heterodimer

Analyse Structure of photosynthetic reaction center with bacteriochlorophyll… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KBY
Type: protein
Length: 819 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosynthetic reaction center protein L chain; Photosynthetic reaction center protein M…
UniProt: P02954, P02953, P11846
Ligands: BCL, BPH, U10, SPO, CDL, FE, CL
Pockets: 14 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Photosynthetic reaction center protein L chain	protein	281	63% helix, 4% strand	P02954
M	Photosynthetic reaction center protein M chain	protein	302	63% helix, 4% strand	P02953
H	Photosynthetic reaction center protein H chain	protein	236	24% helix, 25% strand	P11846

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 3 copies · chains L, M
BPH · Bacteriopheophytin A · ligand · 3 copies · chains L, M
U10 · Ubiquinone-10 · ligand · chains L, M
SPO · Spheroidene · ligand · chains M
CDL · Cardiolipin · ligand · chains L, M, H
FE · Fe (III) ion · metal · chains L, M
CL · Chloride ion · ion · chains M

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1084	0.82	0.82	87	BCL, BPH
2	96	0.75	0.97	29	empty
3	157	0.71	0.89	21	U10
4	51	0.68	0.97	22	empty
5	150	0.60	0.83	29	empty

Interfaces

3 interfaces between chains.

L–M · 4530 Å² buried · 63 hydrogen bonds · protein-protein
M–H · 2800 Å² buried · 35 hydrogen bonds · protein-protein
L–H · 1601 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

1KBY · Structure of Photosynthetic Reaction Center with bacteriochlorophyll-bacteriopheophytin… · the same entry in another collection · chain L against L, TM-score 1.00

Analyse

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

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