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Photosynthetic reaction center mutant from rhodobacter sphaeroides with asp L213 replaced with asn

Analyse Photosynthetic reaction center mutant from rhodobacter sphaeroides with asp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RY5
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, SPO, CDL, FE2, K, PO4
Pockets: 13 · best druggability 0.82

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	62% helix, 4% strand	P02954
M	Reaction center protein M chain	protein	301	64% helix, 4% strand	P02953
H	Reaction center protein H chain	protein	239	23% helix, 25% strand	P11846

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 L, M, H
FE2 · Fe (II) ion · metal · chains L, M
K · Potassium ion · metal · chains H
PO4 · Phosphate ion · ion · 2 copies · chains M, H
LDA · Lauryl dimethylamine-N-oxide · additive · 3 copies · chains L, M, H
GOL · Glycerol · additive · chains L, H

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

Pockets

13 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	1162	0.82	0.82	83	BCL, BPH
2	115	0.77	0.97	34	empty
3	145	0.69	0.89	22	U10
4	105	0.61	0.87	23	U10
5	101	0.58	0.85	19	SPO

Interfaces

3 interfaces between chains.

L–M · 4555 Å² buried · 71 hydrogen bonds · protein-protein
M–H · 2791 Å² buried · 35 hydrogen bonds · protein-protein
L–H · 1615 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

1RY5 · Photosynthetic reaction center mutant from rhodobacter sphaeroides with asp L213 replaced… · 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
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Elsewhere: RCSB PDB 1RY5 · PDBe 1RY5 · UniProt P02954 · UniProt P02953 · UniProt P11846

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