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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: 1Z9K
Type: protein
Length: 821 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: P02954, P02953, P11846
Ligands: BCL, BPH, U10, FE, MN
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Reaction center protein L chain	protein	281	49% helix, 4% strand	P02954
B	Reaction center protein M chain	protein	302	51% helix, 2% strand	P02953
C	Reaction center protein H chain	protein	238	21% helix, 18% strand	P11846

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 4 copies · chains A, B
BPH · Bacteriopheophytin A · ligand · 2 copies · chains A, B
U10 · Ubiquinone-10 · ligand · 2 copies · chains A, B
FE · Fe (III) ion · metal · chains A, B
MN · Manganese (II) ion · metal · chains C

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1183	0.81	0.81	109	BCL
2	285	0.70	0.84	38	U10
3	147	0.59	0.83	19	empty
4	156	0.55	0.81	31	empty
5	148	0.45	0.76	20	empty

Interfaces

3 interfaces between chains.

A–B · 4603 Å² buried · 52 hydrogen bonds · protein-protein
B–C · 2948 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 1696 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1Z9K · Photosynthetic Reaction Center from Rhodobacter sphaeroides · the same entry in another collection · chain A against A, 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 1Z9K · PDBe 1Z9K · UniProt P02954 · UniProt P02953 · UniProt P11846

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