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I(L177)H mutant structure of photosynthetic reaction center from rhodobacter sphaeroides

Analyse I(L177)H mutant structure of photosynthetic reaction center from rhodobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3V3Z
Type: protein
Length: 824 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reaction center protein H chain; Reaction center protein L chain; Reaction center protein…
UniProt: P0C0Y7, P0C0Y8, P0C0Y9
Ligands: BCL, HTO, BPH, U10, SPN, K, FE, PO4, CL
Pockets: 12 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Reaction center protein H chain	protein	241	23% helix, 25% strand	P0C0Y7
L	Reaction center protein L chain	protein	281	62% helix, 3% strand	P0C0Y8
M	Reaction center protein M chain	protein	302	63% helix, 3% strand	P0C0Y9

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
HTO · Heptane-1,2,3-triol · ligand · 3 copies · chains H, M, L
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M
SPN · Speroidenone · ligand · chains M
K · Potassium ion · metal · chains H
FE · Fe (III) ion · metal · chains L, M
PO4 · Phosphate ion · ion · 5 copies · chains H, M, L
CL · Chloride ion · ion · chains M
LDA · Lauryl dimethylamine-N-oxide · additive · 5 copies · chains H, M, L
DIO · 1,4-diethylene dioxide · additive · 2 copies · chains H, M, L

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

Pockets

12 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	775	0.81	0.84	70	BCL
2	113	0.76	0.96	32	empty
3	188	0.73	0.90	41	empty
4	246	0.73	0.87	40	U10
5	100	0.60	0.86	16	empty

Interfaces

3 interfaces between chains.

L–M · 4584 Å² buried · 66 hydrogen bonds · protein-protein
H–M · 2874 Å² buried · 37 hydrogen bonds · protein-protein
H–L · 1620 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

3V3Z · I(L177)H mutant structure of photosynthetic reaction center from Rhodobacter sphaeroides · the same entry in another collection · chain H against H, 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 P0C0Y7
Every structure of UniProt P0C0Y8
Every structure of UniProt P0C0Y9
Elsewhere: RCSB PDB 3V3Z · PDBe 3V3Z · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9

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