Research workbench

(M)L214N mutant of the rhodobacter sphaeroides reaction center

Analyse (M)L214N mutant of the rhodobacter sphaeroides reaction center in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IN7
Type: protein
Length: 823 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, U10, HTO, BPH, GGD, SPO, CDL, PC1, K, FE, MG, PO4
Pockets: 13 · best druggability 0.82

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Reaction center protein H chain	protein	240	23% helix, 25% strand	P0C0Y7
L	Reaction center protein L chain	protein	281	64% helix, 4% strand	P0C0Y8
M	Reaction center protein M chain	protein	302	63% helix, 4% strand	P0C0Y9

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 4 copies · chains L, M
U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M
HTO · Heptane-1,2,3-triol · ligand · 2 copies · chains L
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
GGD · Nonadec-10-enoic acid 2-[3,4-dihydroxy-6-hydroxymethyl-5-(3,4,5-trihydroxy-6-hydroxymethyl-tetrahydro-pyran-2-yloxy)-tetrahydro-pyran-2-yloxy] -1-octadec-9-enoyloxymethyl-ethyl ester · ligand · chains H, L, M
SPO · Spheroidene · ligand · chains M
CDL · Cardiolipin · ligand · chains H, L, M
PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · chains L, M
K · Potassium ion · metal · chains H
FE · Fe (III) ion · metal · chains L, M
MG · Magnesium ion · metal · chains M
PO4 · Phosphate ion · ion · chains L
GOL · Glycerol · additive · 7 copies · chains H, L, M
LDA · Lauryl dimethylamine-N-oxide · additive · 5 copies · chains L, H, M

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

Pockets

13 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	1162	0.82	0.82	91	BCL, MG
2	114	0.78	0.97	32	empty
3	215	0.68	0.85	29	U10
4	220	0.63	0.83	39	empty
5	141	0.59	0.83	24	U10

Interfaces

3 interfaces between chains.

L–M · 4545 Å² buried · 68 hydrogen bonds · protein-protein
H–M · 2798 Å² buried · 38 hydrogen bonds · protein-protein
H–L · 1570 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4IN7 · (M)L214N mutant of the Rhodobacter sphaeroides Reaction Center · 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 4IN7 · PDBe 4IN7 · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9

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