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Photosynthetic reaction center from rhodobacter sphaeroides

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

PDB: 1M3X
Type: protein
Length: 821 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosynthetic reaction center protein L chain; Photosynthetic reaction center protein M…
UniProt: P02954, P02953, P11846
Ligands: BCL, BPH, U10, PC1, SPO, CDL, GGD, FE, CL
Pockets: 13 · best druggability 0.82

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Photosynthetic reaction center protein L chain	protein	281	62% helix, 4% strand	P02954
M	Photosynthetic reaction center protein M chain	protein	302	63% helix, 4% strand	P02953
H	Photosynthetic reaction center protein H chain	protein	238	25% helix, 25% strand	P11846

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
PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · chains L, M
SPO · Spheroidene · ligand · chains M
CDL · Cardiolipin · ligand · chains L, M, H
GGD · Nonadec-10-enoic acid 2-[3,4-dihydroxy-6-hydroxymethyl-5-(3,4,5-trihydroxy-6-hydroxymethyl-tetrahydro-pyran-2-yloxy)-tetrahydro-pyran-2-yloxy] -1-octadec-9-enoyloxymethyl-ethyl ester · ligand · chains L, M, H
FE · Fe (III) ion · metal · chains L, M
CL · Chloride ion · ion · chains M

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

Pockets

13 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	1113	0.82	0.82	86	BCL, BPH
2	110	0.77	0.97	30	empty
3	151	0.70	0.89	21	U10
4	53	0.68	0.96	15	empty
5	126	0.61	0.86	27	U10

Interfaces

3 interfaces between chains.

L–M · 4558 Å² buried · 65 hydrogen bonds · protein-protein
M–H · 2825 Å² buried · 42 hydrogen bonds · protein-protein
L–H · 1598 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

1M3X · Photosynthetic Reaction Center From Rhodobacter Sphaeroides · 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 P02954
Every structure of UniProt P02953
Every structure of UniProt P11846
Elsewhere: RCSB PDB 1M3X · PDBe 1M3X · UniProt P02954 · UniProt P02953 · UniProt P11846

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