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Photosynthetic reaction center from rhodobacter sphaeroides strain rv in surfo crystallization

Analyse Photosynthetic reaction center from rhodobacter sphaeroides strain rv in surfo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z02
Type: protein
Length: 823 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: D12, BCL, MYS, HTO, BPH, U10, D10, SPN, CDL, NA, K, FE, PO4
Pockets: 12 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Reaction center protein H chain	protein	240	25% helix, 23% strand	P0C0Y7
L	Reaction center protein L chain	protein	281	62% helix, 4% strand	P0C0Y8
M	Reaction center protein M chain	protein	302	64% helix, 4% strand	P0C0Y9

Ligands and binding sites

D12 · Dodecane · ligand · 6 copies · chains H, L, M
BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
MYS · Pentadecane · ligand · 3 copies · chains H, L, M
HTO · Heptane-1,2,3-triol · ligand · 3 copies · chains L
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M
D10 · Decane · ligand · chains L
SPN · Speroidenone · ligand · chains M
CDL · Cardiolipin · ligand · chains H, L, M
NA · Sodium ion · metal · chains H, L
K · Potassium ion · metal · chains H
FE · Fe (III) ion · metal · chains L, M
PO4 · Phosphate ion · ion · 3 copies · chains H, M
EDO · 1,2-ethanediol · additive · 13 copies · chains H, L, M
LDA · Lauryl dimethylamine-N-oxide · additive · 7 copies · chains H, L, M
DIO · 1,4-diethylene dioxide · additive · chains L, 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	881	0.83	0.85	83	BCL
2	110	0.78	0.97	31	empty
3	185	0.68	0.86	28	U10
4	107	0.62	0.87	28	U10
5	208	0.61	0.82	39	EDO

Interfaces

3 interfaces between chains.

L–M · 4533 Å² buried · 65 hydrogen bonds · protein-protein
H–M · 2833 Å² buried · 40 hydrogen bonds · protein-protein
H–L · 1622 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6Z02 · Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV in surfo… · the same entry in another collection · chain H against H, TM-score 1.00

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Every structure of UniProt P0C0Y7
Every structure of UniProt P0C0Y8
Every structure of UniProt P0C0Y9
Elsewhere: RCSB PDB 6Z02 · PDBe 6Z02 · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9

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