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E(L212)A,D(L213)A double mutant structure of photosynthetic reaction center from rhodobacter sphaeroides

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

PDB: 1K6N
Type: protein
Length: 823 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosynthetic reaction center L subunit; Photosynthetic reaction center M subunit…
UniProt: P02954, P02953, P11846
Ligands: BCL, BPH, U10, SPN, CDL, FE
Pockets: 15 · best druggability 0.82

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Photosynthetic reaction center L subunit	protein	281	63% helix, 4% strand	P02954
M	Photosynthetic reaction center M subunit	protein	302	64% helix, 4% strand	P02953
H	Photosynthetic reaction center H subunit	protein	240	26% 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
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 · 4 copies · chains L, M, H

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

Pockets

15 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	1170	0.82	0.83	88	BCL
2	95	0.76	0.97	30	empty
3	225	0.73	0.88	39	U10
4	205	0.68	0.85	28	U10
5	50	0.66	0.96	17	empty

Interfaces

3 interfaces between chains.

L–M · 4575 Å² buried · 65 hydrogen bonds · protein-protein
M–H · 2822 Å² buried · 42 hydrogen bonds · protein-protein
L–H · 1613 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1K6N · E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center from… · 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 1K6N · PDBe 1K6N · UniProt P02954 · UniProt P02953 · UniProt P11846

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