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E(L212)A, D(L213)A, A(M249)Y triple mutant structure of photosynthetic reaction center

Analyse E(L212)A, D(L213)A, A(M249)Y triple mutant structure of photosynthetic reaction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DU3
Type: protein
Length: 823 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: P0C0Y8, P0C0Y9, P0C0Y7
Ligands: BCL, BPH, U10, SPN, CDL, FE
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Reaction center protein L chain	protein	281	61% helix, 4% strand	P0C0Y8
M	Reaction center protein M chain	protein	302	61% helix, 4% strand	P0C0Y9
H	Reaction center protein H chain	protein	240	25% helix, 25% strand	P0C0Y7

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 · 3 copies · chains M, H, L

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	1168	0.82	0.82	87	BCL, BPH
2	73	0.74	0.98	29	empty
3	210	0.72	0.88	38	U10
4	185	0.69	0.87	29	U10
5	50	0.67	0.96	16	empty

Interfaces

3 interfaces between chains.

L–M · 4583 Å² buried · 65 hydrogen bonds · protein-protein
M–H · 2904 Å² buried · 47 hydrogen bonds · protein-protein
L–H · 1636 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3DU3 · E(L212)A, D(L213)A, A(M249)Y triple mutant structure of photosynthetic reaction center · 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 P0C0Y8
Every structure of UniProt P0C0Y9
Every structure of UniProt P0C0Y7
Elsewhere: RCSB PDB 3DU3 · PDBe 3DU3 · UniProt P0C0Y8 · UniProt P0C0Y9 · UniProt P0C0Y7

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