MolNFT v1 · #171295 · protein

Photosynthetic reaction center from rhodobacter sphaeroides strain rv in surfo crystallization

6Z02 · Reaction center protein H chain: “Photosynthetic reaction center from rhodobacter sphaeroides strain rv in surfo crystallization”. X-ray diffraction, 13 ligands (D12, BCL, MYS), 12 pockets (best druggability 0.83). MolNFT v1 #171295…

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

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 6Z02 · PDBe 6Z02 · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9

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