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Photosynthetic reaction center mutant with GLUL212 replaced with TRP (chain L, EL212W)

Analyse Photosynthetic reaction center mutant with GLUL212 replaced with TRP (chain L… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LRI
Type: protein
Length: 820 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: Q3J1A5, Q3J1A6, Q3J170
Ligands: BCL, BPH, U10, SPN, CDL, FE
Pockets: 16 · best druggability 0.81

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	64% helix, 4% strand	Q3J1A5
M	Reaction center protein M chain	protein	300	64% helix, 4% strand	Q3J1A6
H	Reaction center protein H chain	protein	239	25% helix, 24% strand	Q3J170

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
SPN · Speroidenone · ligand · chains M
CDL · Cardiolipin · ligand · chains L, M, H
FE · Fe (III) ion · metal · chains L, M
LDA · Lauryl dimethylamine-N-oxide · additive · 5 copies · chains L, M, H
DD9 · nonane · additive · 3 copies · chains L, H

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

Pockets

16 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	739	0.81	0.84	55	BCL
2	105	0.76	0.96	30	empty
3	55	0.69	0.97	17	empty
4	178	0.68	0.87	31	U10
5	128	0.60	0.84	21	U10

Interfaces

3 interfaces between chains.

L–M · 4590 Å² buried · 71 hydrogen bonds · protein-protein
M–H · 2750 Å² buried · 35 hydrogen bonds · protein-protein
L–H · 1617 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

5LRI · Photosynthetic reaction center mutant with GLUL212 replaced with TRP (chain L, EL212W) · the same entry in another collection · chain L against L, TM-score 1.00
Q3J1A5 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (Q3J1A5) · a predicted model of the same protein · chain L against A, TM-score 1.00
Q3J1A6 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (Q3J1A6) · a predicted model of the same protein · chain M against A, TM-score 1.00
Q3J170 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (Q3J170) · a predicted model of the same protein · chain H against A, TM-score 0.98

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 Q3J1A5
Every structure of UniProt Q3J1A6
Every structure of UniProt Q3J170
Elsewhere: RCSB PDB 5LRI · PDBe 5LRI · UniProt Q3J1A5 · UniProt Q3J1A6 · UniProt Q3J170

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