MolNFT v1 · #38998 · protein

Reaction centre from rhodobacter sphaeroides strain R-26.1 complexed with brominated phosphatidylcholine

2HG3 · Reaction center protein L chain: “Reaction centre from rhodobacter sphaeroides strain R-26.1 complexed with brominated phosphatidylcholine”. X-ray diffraction, 9 ligands (BCL, BPH, U10), 12 pockets (best druggability 0.82). MolNFT…

PDB: 2HG3
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: P0C0Y8, P0C0Y9, P0C0Y7
Ligands: BCL, BPH, U10, PC9, HTO, CDL, FE, K, PO4
Pockets: 12 · best druggability 0.82

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	64% helix, 4% strand	P0C0Y8
M	Reaction center protein M chain	protein	302	64% helix, 4% strand	P0C0Y9
H	Reaction center protein H chain	protein	240	25% helix, 26% strand	P0C0Y7

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
PC9 · (7R,14S)-14,15-dibromo-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · 2 copies · chains L, M, H
HTO · Heptane-1,2,3-triol · ligand · chains L, M, H
CDL · Cardiolipin · ligand · chains L, M, H
FE · Fe (III) ion · metal · chains L, M
K · Potassium ion · metal · chains H
PO4 · Phosphate ion · ion · 4 copies · chains L, H, M
LDA · Lauryl dimethylamine-N-oxide · additive · 10 copies · chains L, H, M
GOL · Glycerol · additive · 4 copies · chains L, H, M

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

Pockets

12 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	1179	0.82	0.82	88	BCL, LDA
2	129	0.78	0.97	35	empty
3	180	0.76	0.91	37	U10
4	55	0.68	0.96	15	empty
5	164	0.62	0.83	29	U10

Interfaces

3 interfaces between chains.

L–M · 4565 Å² buried · 71 hydrogen bonds · protein-protein
M–H · 2823 Å² buried · 45 hydrogen bonds · protein-protein
L–H · 1599 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

2HG3 · Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with brominated… · the same entry in another collection · chain L against L, TM-score 1.00
P0C0Y8 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (P0C0Y8) · a predicted model of the same protein · chain L against A, TM-score 1.00
P0C0Y9 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (P0C0Y9) · a predicted model of the same protein · chain M against A, TM-score 1.00
P0C0Y7 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (P0C0Y7) · a predicted model of the same protein · chain H against A, TM-score 0.98

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 P0C0Y8
Every structure of UniProt P0C0Y9
Every structure of UniProt P0C0Y7
Elsewhere: RCSB PDB 2HG3 · PDBe 2HG3 · UniProt P0C0Y8 · UniProt P0C0Y9 · UniProt P0C0Y7

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