MolNFT v1 · #120767 · protein

Structure function studies of R. palustris rubisco (S59F/M331A mutant; cabp-bound)

5HAT · Ribulose bisphosphate carboxylase: “Structure function studies of R. palustris rubisco (S59F/M331A mutant; cabp-bound)”. X-ray diffraction, 2 ligands (CAP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #120767 on GenesisL1: 3D…

PDB: 5HAT
Type: protein
Length: 5,467 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribulose bisphosphate carboxylase
EC: 4.1.1.39
UniProt: Q6N0W9
Ligands: CAP, MG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, I, J, K	Ribulose bisphosphate carboxylase (EC 4.1.1.39)	protein	455	44% helix, 18% strand	Q6N0W9
E, L	Ribulose bisphosphate carboxylase (EC 4.1.1.39)	protein	457	44% helix, 18% strand	Q6N0W9
F, G, H	Ribulose bisphosphate carboxylase (EC 4.1.1.39)	protein	456	44% helix, 18% strand	Q6N0W9

Ligands and binding sites

CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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	956	0.83	0.85	102	empty
2	798	0.83	0.86	80	empty
3	931	0.83	0.84	97	empty
4	966	0.83	0.84	113	empty
5	978	0.82	0.84	112	empty

Interfaces

27 interfaces between chains.

E–F · 4268 Å² buried · 64 hydrogen bonds · protein-protein
C–D · 4266 Å² buried · 65 hydrogen bonds · protein-protein
G–H · 4262 Å² buried · 64 hydrogen bonds · protein-protein
K–L · 4260 Å² buried · 65 hydrogen bonds · protein-protein
I–J · 4244 Å² buried · 64 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (carboxylation).

Compared structures

5HAT · Structure function studies of R. palustris RubisCO (S59F/M331A mutant; CABP-bound) · 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 Q6N0W9
Elsewhere: RCSB PDB 5HAT · PDBe 5HAT · UniProt Q6N0W9

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.