MolNFT v1 · #93928 · protein

Structure of pisum sativum rubisco

4HHH · Ribulose bisphosphate carboxylase large chain: “Structure of pisum sativum rubisco”. X-ray diffraction, 1 ligand (RUB), 20 pockets (best druggability 0.75). MolNFT v1 #93928 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4HHH
Type: protein
Length: 2,324 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase small…
EC: 4.1.1.39
UniProt: P04717
Ligands: RUB
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39)	protein	458	42% helix, 17% strand	P04717
S, T, U, V	Ribulose bisphosphate carboxylase small chain	protein	123	21% helix, 22% strand	—

Ligands and binding sites

RUB · Ribulose-1,5-diphosphate · ligand · 4 copies · chains A, B, C, D

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	76	0.75	0.98	21	empty
2	68	0.73	0.98	22	empty
3	54	0.71	0.98	16	empty
4	55	0.70	0.97	17	empty
5	252	0.67	0.83	42	RUB

Interfaces

16 interfaces between chains.

B–T · 2077 Å² buried · 25 hydrogen bonds · protein-protein
D–V · 2008 Å² buried · 26 hydrogen bonds · protein-protein
A–S · 1953 Å² buried · 22 hydrogen bonds · protein-protein
C–U · 1914 Å² buried · 16 hydrogen bonds · protein-protein
C–T · 1022 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4HHH · Structure of Pisum sativum Rubisco · the same entry in another collection · chain V against V, TM-score 1.00
P04717 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain A against A, 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 P04717
Elsewhere: RCSB PDB 4HHH · PDBe 4HHH · UniProt P04717

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