MolNFT v1 · #66897 · protein

Photosynthetic reaction center from rhodobacter sphaeroides 2.4.1

3I4D · Reaction center protein L chain: “Photosynthetic reaction center from rhodobacter sphaeroides 2.4.1”. X-ray diffraction, 12 ligands (BCL, BPH, U10), 13 pockets (best druggability 0.83). MolNFT v1 #66897 on GenesisL1: 3D structure…

PDB: 3I4D
Type: protein
Length: 822 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, HTO, UQ1, HT3, SPO, CDL, K, FE, PO4, CL
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Reaction center protein L chain	protein	281	63% helix, 3% strand	P0C0Y8
M	Reaction center protein M chain	protein	302	65% helix, 4% strand	P0C0Y9
H	Reaction center protein H chain	protein	239	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
HTO · Heptane-1,2,3-triol · ligand · 2 copies · chains L, H
UQ1 · Ubiquinone-1 · ligand · chains L, M
HT3 · (2R,3S)-heptane-1,2,3-triol · ligand · chains L
SPO · Spheroidene · ligand · chains M
CDL · Cardiolipin · ligand · chains L, M, H
K · Potassium ion · metal · 2 copies · chains M, H
FE · Fe (III) ion · metal · chains L, M
PO4 · Phosphate ion · ion · 7 copies · chains L, H, M
CL · Chloride ion · ion · chains M, H
GOL · Glycerol · additive · 26 copies · chains L, H, M
LDA · Lauryl dimethylamine-N-oxide · additive · 21 copies · chains L, M, H
DIO · 1,4-diethylene dioxide · additive · chains L

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

Pockets

13 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	891	0.83	0.84	74	BCL, SPO
2	118	0.78	0.97	31	empty
3	184	0.69	0.87	27	empty
4	51	0.67	0.96	14	empty
5	121	0.61	0.86	29	empty

Interfaces

3 interfaces between chains.

L–M · 4489 Å² buried · 65 hydrogen bonds · protein-protein
M–H · 2807 Å² buried · 43 hydrogen bonds · protein-protein
L–H · 1590 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3I4D · Photosynthetic reaction center from rhodobacter sphaeroides 2.4.1 · 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 P0C0Y8
Every structure of UniProt P0C0Y9
Every structure of UniProt P0C0Y7
Elsewhere: RCSB PDB 3I4D · PDBe 3I4D · UniProt P0C0Y8 · UniProt P0C0Y9 · UniProt P0C0Y7

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