MolNFT v1 · #13369 · protein

X-ray structure of the cytochrome-C(2)-photosynthetic reaction center electron transfer complex from rhodobacter sphaeroides in type II co- crystals

1L9B · Reaction center protein L chain: “X-ray structure of the cytochrome-C(2)-photosynthetic reaction center electron transfer complex from…”. X-ray diffraction, 8 ligands (BCL, BPH, HTO), 14 pockets (best druggability 0.83). MolNFT v1…

PDB: 1L9B
Type: protein
Length: 918 residues
Chains: 4
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, P00095
Ligands: BCL, BPH, HTO, U10, HEM, NA, FE2, CL
Pockets: 14 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 8% 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	267	73% helix, 3% strand	P02953
H	Reaction center protein H chain	protein	246	23% helix, 21% strand	P11846
C	Cytochrome C-2	protein	124	43% helix, 7% strand	P00095

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
HTO · Heptane-1,2,3-triol · ligand · 2 copies · chains L, M, H, C
U10 · Ubiquinone-10 · ligand · chains L, M
HEM · Protoporphyrin IX containing Fe · ligand · chains L, M, C
NA · Sodium ion · metal · chains L, M
FE2 · Fe (II) ion · metal · chains L, M
CL · Chloride ion · ion · chains L, M
LDA · Lauryl dimethylamine-N-oxide · additive · 9 copies · chains L, M, H

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	877	0.83	0.84	74	BCL, BPH
2	594	0.79	0.84	90	HEM, HTO
3	836	0.74	0.79	64	empty
4	303	0.74	0.87	61	empty
5	184	0.70	0.87	22	U10

Interfaces

5 interfaces between chains.

L–M · 3903 Å² buried · 49 hydrogen bonds · protein-protein
M–H · 1847 Å² buried · 27 hydrogen bonds · protein-protein
L–H · 1508 Å² buried · 14 hydrogen bonds · protein-protein
M–C · 442 Å² buried · 3 hydrogen bonds · protein-protein
L–C · 305 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 cofactor (heme attachment).

Compared structures

1L9B · X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer… · 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
Every structure of UniProt P00095
Elsewhere: RCSB PDB 1L9B · PDBe 1L9B · UniProt P02954 · UniProt P02953 · UniProt P11846 · UniProt P00095

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