MolNFT v1 · #20369 · protein

Spinach rubisco in complex with the inhibitor D-xylulose-2, 2-diol-1,5-bisphosphate

1RCO · Ribulose bisphosphate CARBOXYLASE/OXYGENASE: “Spinach rubisco in complex with the inhibitor D-xylulose-2, 2-diol-1,5-bisphosphate”. X-ray diffraction, 1 ligand (XDP), 20 pockets (best druggability 0.85). MolNFT v1 #20369 on…

PDB: 1RCO
Type: protein
Length: 4,720 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribulose bisphosphate CARBOXYLASE/OXYGENASE
EC: 4.1.1.39
UniProt: P00875, P00870
Ligands: XDP
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, B, E, H, K, O, R, V	Ribulose bisphosphate CARBOXYLASE/OXYGENASE (EC 4.1.1.39)	protein	467	43% helix, 17% strand	P00875
S, C, F, I, M, P, T, W	Ribulose bisphosphate CARBOXYLASE/OXYGENASE (EC 4.1.1.39)	protein	123	22% helix, 24% strand	P00870

Ligands and binding sites

XDP · D-xylulose-2,2-diol-1,5-bisphosphate · ligand · 8 copies · chains L, B, E, H, K, O, R, V

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1005	0.85	0.86	116	empty
2	1044	0.84	0.86	120	empty
3	1055	0.84	0.86	118	empty
4	185	0.83	0.97	44	XDP
5	177	0.82	0.98	45	XDP

Interfaces

48 interfaces between chains.

E–H · 4806 Å² buried · 78 hydrogen bonds · protein-protein
K–O · 4773 Å² buried · 76 hydrogen bonds · protein-protein
L–B · 4765 Å² buried · 76 hydrogen bonds · protein-protein
R–V · 4730 Å² buried · 71 hydrogen bonds · protein-protein
V–W · 1924 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1RCO · Spinach rubisco in complex with the inhibitor D-xylulose-2,2-diol-1,5-bisphosphate · the same entry in another collection · chain W against W, 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 P00875
Every structure of UniProt P00870
Elsewhere: RCSB PDB 1RCO · PDBe 1RCO · UniProt P00875 · UniProt P00870

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