MolNFT v1 · #53523 · protein

Hexa-coordination of a bacteriochlorophyll cofactor in the rhodobacter sphaeroides reaction centre

2WX5 · Reaction center protein H chain: “Hexa-coordination of a bacteriochlorophyll cofactor in the rhodobacter sphaeroides reaction centre”. X-ray diffraction, 8 ligands (BCL, HTO, BPH), 16 pockets (best druggability 0.82). MolNFT v1…

PDB: 2WX5
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 centre protein L chain; Reaction centre protein…
UniProt: P0C0Y7, P0C0Y8, P0C0Y9
Ligands: BCL, HTO, BPH, CDL, SPN, U10, NA, FE
Pockets: 16 · 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	26% helix, 25% strand	P0C0Y7
L	Reaction centre protein L chain	protein	281	60% helix, 3% strand	P0C0Y8
M	Reaction centre protein M chain	protein	302	64% helix, 4% 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 L, M
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
CDL · Cardiolipin · ligand · chains H, L, M
SPN · Speroidenone · ligand · chains M
U10 · Ubiquinone-10 · ligand · chains L, M
NA · Sodium ion · metal · 2 copies · chains H, M
FE · Fe (III) ion · metal · chains L, M
LDA · Lauryl dimethylamine-N-oxide · additive · 6 copies · chains H, L, M
GOL · Glycerol · additive · 2 copies · chains H, L

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

Pockets

16 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	818	0.82	0.84	66	BCL
2	111	0.77	0.97	34	empty
3	258	0.75	0.88	47	U10
4	57	0.70	0.97	15	empty
5	150	0.61	0.84	29	HTO

Interfaces

3 interfaces between chains.

L–M · 4571 Å² buried · 60 hydrogen bonds · protein-protein
H–M · 2841 Å² buried · 35 hydrogen bonds · protein-protein
H–L · 1617 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

2WX5 · Hexa-coordination of a bacteriochlorophyll cofactor in the 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 2WX5 · PDBe 2WX5 · UniProt P0C0Y7 · UniProt P0C0Y8 · UniProt P0C0Y9

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