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Crystal structure of R. sphaeroides photosynthetic reaction center variant; Y(M210)3-methyltyrosine

Analyse Crystal structure of R. sphaeroides photosynthetic reaction center variant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MH8
Type: protein
Length: 821 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: P0C0Y7, P0C0Y8, P0C0Y9
Ligands: BCL, BPH, U10, SPO, CDL, FE
Pockets: 11 · best druggability 0.82

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Reaction center protein H chain	protein	239	25% helix, 26% strand	P0C0Y7
L	Reaction center protein L chain	protein	281	62% helix, 4% strand	P0C0Y8
M	Reaction center protein M chain	protein	301	63% helix, 4% strand	P0C0Y9

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
SPO · Spheroidene · ligand · chains M
CDL · Cardiolipin · ligand · chains H, L, M
FE · Fe (III) ion · metal · chains L, M
LDA · Lauryl dimethylamine-N-oxide · additive · 5 copies · chains H, M, L

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

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1194	0.82	0.82	91	BCL, SPO
2	126	0.77	0.96	33	empty
3	197	0.67	0.85	27	U10
4	174	0.62	0.84	29	U10
5	104	0.51	0.82	21	BPH

Interfaces

3 interfaces between chains.

L–M · 4582 Å² buried · 63 hydrogen bonds · protein-protein
H–M · 2845 Å² buried · 44 hydrogen bonds · protein-protein
H–L · 1596 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nonstandard).

Compared structures

7MH8 · Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant… · the same entry in another collection · chain H against H, 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 P0C0Y7
Every structure of UniProt P0C0Y8
Every structure of UniProt P0C0Y9
Elsewhere: RCSB PDB 7MH8 · PDBe 7MH8 · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9

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