MolNFT v1 · #81821 · protein

Photosynthetic reaction center from rhodobacter sphaeroides strain rv

3V3Y · Reaction center protein H chain: “Photosynthetic reaction center from rhodobacter sphaeroides strain rv”. X-ray diffraction, 7 ligands (BCL, BPH, U10), 10 pockets (best druggability 0.81). MolNFT v1 #81821 on GenesisL1: 3D…

PDB: 3V3Y
Type: protein
Length: 824 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reaction center protein H chain; Reaction center protein L chain; Reaction center protein…
UniProt: P0C0Y7, P0C0Y8, P0C0Y9
Ligands: BCL, BPH, U10, SPN, FE, PO4, CL
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Reaction center protein H chain	protein	241	24% helix, 22% strand	P0C0Y7
L	Reaction center protein L chain	protein	281	60% helix, 4% strand	P0C0Y8
M	Reaction center protein M chain	protein	302	65% helix, 4% strand	P0C0Y9

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
SPN · Speroidenone · ligand · chains M
FE · Fe (III) ion · metal · chains L, M
PO4 · Phosphate ion · ion · 3 copies · chains H, L, M
CL · Chloride ion · ion · chains M
LDA · Lauryl dimethylamine-N-oxide · additive · 8 copies · chains H, M, L
DIO · 1,4-diethylene dioxide · additive · 3 copies · chains L, M

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1176	0.81	0.82	90	BCL, BPH
2	102	0.77	0.98	31	empty
3	167	0.75	0.92	39	U10
4	151	0.63	0.85	28	U10
5	110	0.59	0.85	19	empty

Interfaces

3 interfaces between chains.

L–M · 4534 Å² buried · 67 hydrogen bonds · protein-protein
H–M · 2867 Å² buried · 39 hydrogen bonds · protein-protein
H–L · 1655 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

3V3Y · Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV · the same entry in another collection · chain H against H, 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 P0C0Y7
Every structure of UniProt P0C0Y8
Every structure of UniProt P0C0Y9
Elsewhere: RCSB PDB 3V3Y · PDBe 3V3Y · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9

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