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Crystal structure analysis of the mutant reaction center pro L209-> tyr from the photosynthetic purple bacterium rhodobacter sphaeroides

Analyse Crystal structure analysis of the mutant reaction center pro L209-> tyr from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1F6N
Type: protein
Length: 823 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, BPH, U10, SPO, FE, PO4
Pockets: 11 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Reaction center protein L chain	protein	281	61% helix, 3% strand	P02954
M	Reaction center protein M chain	protein	302	62% helix, 3% strand	P02953
H	Reaction center protein H chain	protein	240	22% helix, 23% strand	P11846

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M
SPO · Spheroidene · ligand · chains M
FE · Fe (III) ion · metal · chains L, M
PO4 · Phosphate ion · ion · chains L, M, H
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

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1166	0.82	0.82	87	BCL
2	112	0.78	0.98	34	empty
3	255	0.75	0.88	43	U10
4	193	0.69	0.86	39	U10
5	140	0.60	0.84	18	SPO

Interfaces

3 interfaces between chains.

L–M · 4619 Å² buried · 60 hydrogen bonds · protein-protein
M–H · 2874 Å² buried · 42 hydrogen bonds · protein-protein
L–H · 1617 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

1F6N · Crystal structure analysis of the mutant reaction center pro L209-> tyr from the… · the same entry in another collection · chain L against L, 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 P02954
Every structure of UniProt P02953
Every structure of UniProt P11846
Elsewhere: RCSB PDB 1F6N · PDBe 1F6N · UniProt P02954 · UniProt P02953 · UniProt P11846

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