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F(M197)H mutant structure of photosynthetic reaction center from rhodobacter sphaeroides strain rv by fixed-target serial synchrotron crystallography (room temperature, 26KEV)

Analyse F(M197)H mutant structure of photosynthetic reaction center from rhodobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7P2C
Type: protein
Length: 822 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: Q3J170, Q3J1A5, Q3J1A6
Ligands: BCL, MYS, BPH, NKP, U10, SPN, FE, PO4
Pockets: 16 · best druggability 0.81

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	239	26% helix, 24% strand	Q3J170
L	Reaction center protein L chain	protein	281	63% helix, 4% strand	Q3J1A5
M	Reaction center protein M chain	protein	302	63% helix, 3% strand	Q3J1A6

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
MYS · Pentadecane · ligand · 3 copies · chains L, M, H
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
NKP · (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate · ligand · 2 copies · chains H, L, M
U10 · Ubiquinone-10 · ligand · chains H, L, M
SPN · Speroidenone · ligand · chains M
FE · Fe (III) ion · metal · chains L, M
PO4 · Phosphate ion · ion · chains M
LDA · Lauryl dimethylamine-N-oxide · additive · 2 copies · chains H, M, L
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains L, M
EDO · 1,2-ethanediol · additive · chains H, M

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

Pockets

16 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	814	0.81	0.84	71	BCL
2	176	0.77	0.92	35	empty
3	73	0.72	0.97	26	empty
4	111	0.65	0.89	25	OLC
5	101	0.57	0.85	19	empty

Interfaces

3 interfaces between chains.

L–M · 4600 Å² buried · 67 hydrogen bonds · protein-protein
H–M · 2864 Å² buried · 41 hydrogen bonds · protein-protein
H–L · 1575 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

7P2C · F(M197)H mutant structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides… · the same entry in another collection · chain H against H, 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 0.99
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 0.99
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 Q3J170
Every structure of UniProt Q3J1A5
Every structure of UniProt Q3J1A6
Elsewhere: RCSB PDB 7P2C · PDBe 7P2C · UniProt Q3J170 · UniProt Q3J1A5 · UniProt Q3J1A6

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