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Photosynthetic reaction center double mutant from rhodobacter sphaeroides with asp L213 replaced with asn and arg H177 replaced with his

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: 1RVJ
Type: protein
Length: 820 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, PO4
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Reaction center protein L chain	protein	281	63% helix, 4% strand	P02954
M	Reaction center protein M chain	protein	301	65% helix, 4% strand	P02953
H	Reaction center protein H chain	protein	238	25% 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
PO4 · Phosphate ion · ion · chains M
LDA · Lauryl dimethylamine-N-oxide · additive · 3 copies · chains L, M, 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	911	0.83	0.84	83	BCL
2	209	0.68	0.85	30	U10
3	93	0.58	0.87	19	empty
4	91	0.55	0.84	21	empty
5	134	0.46	0.78	27	empty

Interfaces

3 interfaces between chains.

L–M · 4506 Å² buried · 67 hydrogen bonds · protein-protein
M–H · 2907 Å² buried · 38 hydrogen bonds · protein-protein
L–H · 1637 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1RVJ · 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

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P02954
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Elsewhere: RCSB PDB 1RVJ · PDBe 1RVJ · UniProt P02954 · UniProt P02953 · UniProt P11846

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