Research workbench

From macrocrystals to microcrystals: a strategy for membrane protein serial crystallography

Analyse From macrocrystals to microcrystals: a strategy for membrane protein serial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NJ4
Type: protein
Length: 1,186 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosynthetic reaction center cytochrome C subunit; Reaction center protein H chain…
UniProt: P07173, P06008, P06009, P06010
Ligands: HEC, BCB, HTO, BPB, DGA, MQ7, NS5, FE2, SO4
Pockets: 17 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Photosynthetic reaction center cytochrome C subunit	protein	332	42% helix, 4% strand	P07173
H	Reaction center protein H chain	protein	258	25% helix, 23% strand	P06008
L	Reaction center protein L chain	protein	273	66% helix, 4% strand	P06009
M	Reaction center protein M chain	protein	323	63% helix, 5% strand	P06010

Ligands and binding sites

HEC · Heme C · ligand · 4 copies · chains C, L, M
BCB · Bacteriochlorophyll B · ligand · 4 copies · chains L, M
HTO · Heptane-1,2,3-triol · ligand · 3 copies · chains H, M, C, L
BPB · Bacteriopheophytin B · ligand · 2 copies · chains L, M
DGA · Diacyl glycerol · ligand · chains C, L, M
MQ7 · Menaquinone-7 · ligand · chains L, M
NS5 · 15-cis-1,2-dihydroneurosporene · ligand · chains M
FE2 · Fe (II) ion · metal · chains L, M
SO4 · Sulfate ion · ion · 15 copies · chains C, M, L, H
LDA · Lauryl dimethylamine-N-oxide · additive · 7 copies · chains H, M, L

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

Pockets

17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1040	0.87	0.88	128	HEC
2	1182	0.83	0.83	98	LDA, BCB, BPB
3	79	0.75	0.98	24	empty
4	53	0.71	0.99	24	empty
5	178	0.68	0.86	22	MQ7

Interfaces

6 interfaces between chains.

L–M · 4430 Å² buried · 57 hydrogen bonds · protein-protein
H–M · 2901 Å² buried · 47 hydrogen bonds · protein-protein
C–M · 2745 Å² buried · 37 hydrogen bonds · protein-protein
H–L · 1904 Å² buried · 20 hydrogen bonds · protein-protein
C–L · 1793 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor, 1 covalent, 1 modified (heme c attachment, covalent ligand, formylation).

Compared structures

5NJ4 · From macrocrystals to microcrystals: a strategy for membrane protein serial… · the same entry in another collection · chain M against M, TM-score 1.00
P07173 · AlphaFold monomer V2.0 prediction for photosynthetic reaction center cytochrome C subunit… · a predicted model of the same protein · chain C against A, TM-score 1.00
P06009 · AlphaFold monomer V2.0 prediction for reaction center protein L chain (P06009) · a predicted model of the same protein · chain L against A, TM-score 0.99
P06010 · AlphaFold monomer V2.0 prediction for reaction center protein M chain (P06010) · a predicted model of the same protein · chain M against A, TM-score 0.97
P06008 · AlphaFold monomer V2.0 prediction for reaction center protein H chain (P06008) · a predicted model of the same protein · chain H against A, TM-score 0.94

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 P07173
Every structure of UniProt P06008
Every structure of UniProt P06009
Every structure of UniProt P06010
Elsewhere: RCSB PDB 5NJ4 · PDBe 5NJ4 · UniProt P07173 · UniProt P06008 · UniProt P06009 · UniProt P06010

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.