MolNFT v1 · #95338 · protein

(M)L214G mutant of the rhodobacter sphaeroides reaction center

4IN5 · Reaction center protein L chain: “(M)L214G mutant of the rhodobacter sphaeroides reaction center”. X-ray diffraction, 9 ligands (BCL, BPH, U10), 13 pockets (best druggability 0.82). MolNFT v1 #95338 on GenesisL1: 3D structure…

PDB: 4IN5
Type: protein
Length: 823 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reaction center protein L chain; Reaction center protein M chain; Reaction center protein…
UniProt: P0C0Y8, P0C0Y9, P0C0Y7
Ligands: BCL, BPH, U10, HTO, SPO, PC1, FE, K, 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
L	Reaction center protein L chain	protein	281	64% helix, 4% strand	P0C0Y8
M	Reaction center protein M chain	protein	302	64% helix, 4% strand	P0C0Y9
H	Reaction center protein H chain	protein	240	25% helix, 25% strand	P0C0Y7

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
HTO · Heptane-1,2,3-triol · ligand · 2 copies · chains L, H
SPO · Spheroidene · ligand · chains M
PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · chains L, M
FE · Fe (III) ion · metal · chains L, M
K · Potassium ion · metal · chains H
PO4 · Phosphate ion · ion · 3 copies · chains L, M
GOL · Glycerol · additive · 12 copies · chains L, H, M
LDA · Lauryl dimethylamine-N-oxide · additive · 6 copies · chains L, M, H

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	860	0.82	0.84	81	BCL
2	115	0.78	0.98	33	empty
3	127	0.69	0.90	19	U10
4	231	0.64	0.82	42	GOL
5	139	0.59	0.83	28	U10

Interfaces

3 interfaces between chains.

L–M · 4554 Å² buried · 71 hydrogen bonds · protein-protein
M–H · 2795 Å² buried · 41 hydrogen bonds · protein-protein
L–H · 1582 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4IN5 · (M)L214G mutant of the Rhodobacter sphaeroides Reaction Center · 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 P0C0Y8
Every structure of UniProt P0C0Y9
Every structure of UniProt P0C0Y7
Elsewhere: RCSB PDB 4IN5 · PDBe 4IN5 · UniProt P0C0Y8 · UniProt P0C0Y9 · UniProt P0C0Y7

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