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Crystal structure of new trigonal form of photosynthetic reaction center from blastochloris viridis. crystals grown in microfluidics by detergent capture.

Analyse Crystal structure of new trigonal form of photosynthetic reaction center from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3D38
Type: protein
Length: 1,178 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, UQ1, MQ9, NS5, FE2, SO4
Pockets: 18 · best druggability 0.88

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Photosynthetic reaction center cytochrome C subunit	protein	332	40% helix, 3% strand	P07173
H	Reaction center protein H chain	protein	250	26% helix, 25% strand	P06008
L	Reaction center protein L chain	protein	273	65% helix, 4% strand	P06009
M	Reaction center protein M chain	protein	323	61% helix, 4% 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 C, H, M
BPB · Bacteriopheophytin B · ligand · 2 copies · chains L, M
UQ1 · Ubiquinone-1 · ligand · 2 copies · chains L, M
MQ9 · Menaquinone-9 · 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, L, M, H
LDA · Lauryl dimethylamine-N-oxide · additive · 4 copies · chains H, M, L

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

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	918	0.88	0.89	113	HEC
2	919	0.84	0.85	93	BCB, LDA
3	109	0.77	0.97	33	empty
4	212	0.75	0.90	35	empty
5	56	0.70	0.98	22	empty

Interfaces

6 interfaces between chains.

L–M · 4398 Å² buried · 63 hydrogen bonds · protein-protein
H–M · 2851 Å² buried · 46 hydrogen bonds · protein-protein
C–M · 2733 Å² buried · 36 hydrogen bonds · protein-protein
H–L · 1858 Å² buried · 19 hydrogen bonds · protein-protein
C–L · 1756 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 cofactor, 1 modified (heme c attachment, formylation).

Compared structures

3D38 · Crystal structure of new trigonal form of photosynthetic reaction center from… · 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 0.96

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
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Every structure of UniProt P06010
Elsewhere: RCSB PDB 3D38 · PDBe 3D38 · UniProt P07173 · UniProt P06008 · UniProt P06009 · UniProt P06010

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