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

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

PDB: 1FNP
Type: protein
Length: 822 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: 16 · 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	62% helix, 3% strand	P02954
M	Reaction center protein M chain	protein	301	62% helix, 4% strand	P02953
H	Reaction center protein H chain	protein	240	22% helix, 24% 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
LDA · Lauryl dimethylamine-N-oxide · additive · 7 copies · chains L, M, H

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

Pockets

16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	823	0.82	0.84	69	BCL
2	103	0.76	0.97	32	empty
3	202	0.72	0.88	44	empty
4	50	0.69	0.98	23	empty
5	208	0.69	0.86	29	U10

Interfaces

3 interfaces between chains.

L–M · 4609 Å² buried · 64 hydrogen bonds · protein-protein
M–H · 2837 Å² buried · 35 hydrogen bonds · protein-protein
L–H · 1626 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

1FNP · Crystal structure analysis of the mutant reaction center pro L209-> phe 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
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Elsewhere: RCSB PDB 1FNP · PDBe 1FNP · UniProt P02954 · UniProt P02953 · UniProt P11846

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