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Photosynthetic reaction center double mutant from rhodobacter sphaeroides with asp L213 replaced with asn and arg M233 replaced with cys in the charge-separated D+QAQB- state

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

PDB: 1S00
Type: protein
Length: 1,654 residues
Chains: 6
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, FE2
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 55% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, R	Reaction center protein L chain	protein	281	62% helix, 4% strand	P02954
M	Reaction center protein M chain	protein	301	63% helix, 4% strand	P02953
H, T	Reaction center protein H chain	protein	246	26% helix, 24% strand	P11846
S	Reaction center protein M chain	protein	299	65% helix, 4% strand	P02953

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 8 copies · chains L, M, R, S
BPH · Bacteriopheophytin A · ligand · 4 copies · chains L, M, R, S
U10 · Ubiquinone-10 · ligand · 4 copies · chains L, M, R, S
SPO · Spheroidene · ligand · 2 copies · chains M, S
FE2 · Fe (II) ion · metal · 2 copies · chains L, M, R, S
LDA · Lauryl dimethylamine-N-oxide · additive · chains M

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	930	0.84	0.85	83	BCL, BPH
2	884	0.83	0.85	85	BCL, BPH
3	197	0.75	0.91	44	U10
4	134	0.67	0.88	21	U10
5	181	0.67	0.86	43	empty

Interfaces

6 interfaces between chains.

L–M · 4532 Å² buried · 65 hydrogen bonds · protein-protein
R–S · 4522 Å² buried · 72 hydrogen bonds · protein-protein
M–H · 2832 Å² buried · 35 hydrogen bonds · protein-protein
S–T · 2734 Å² buried · 36 hydrogen bonds · protein-protein
L–H · 1642 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

1S00 · Photosynthetic reaction center double mutant from rhodobacter sphaeroides with asp L213… · the same entry in another collection · chain L against L, TM-score 1.00

Analyse

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Every structure of UniProt P02954
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Elsewhere: RCSB PDB 1S00 · PDBe 1S00 · UniProt P02954 · UniProt P02953 · UniProt P11846

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