MolNFT v1 · #124770 · protein

Structure function studies of R. palustris rubisco (K192C mutant; cabp-bound)

5KOZ · Ribulose bisphosphate carboxylase: “Structure function studies of R. palustris rubisco (K192C mutant; cabp-bound)”. X-ray diffraction, 3 ligands (CAP, MG, CO3), 20 pockets (best druggability 0.84). MolNFT v1 #124770 on GenesisL1: 3D…

PDB: 5KOZ
Type: protein
Length: 5,464 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, CO3
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, F, G, H, I, J, L	Ribulose bisphosphate carboxylase (EC 4.1.1.39)	protein	455	44% helix, 18% strand	Q6N0W9
C	Ribulose bisphosphate carboxylase (EC 4.1.1.39)	protein	457	45% helix, 18% strand	Q6N0W9
D, K	Ribulose bisphosphate carboxylase (EC 4.1.1.39)	protein	456	45% 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
CO3 · Carbonate ion · ion · 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	1053	0.84	0.85	118	empty
2	893	0.84	0.86	82	empty
3	1038	0.83	0.84	111	empty
4	929	0.83	0.85	97	empty
5	962	0.82	0.84	92	empty

Interfaces

27 interfaces between chains.

E–F · 4257 Å² buried · 67 hydrogen bonds · protein-protein
K–L · 4247 Å² buried · 65 hydrogen bonds · protein-protein
A–B · 4225 Å² buried · 67 hydrogen bonds · protein-protein
C–D · 4214 Å² buried · 67 hydrogen bonds · protein-protein
G–H · 4211 Å² buried · 66 hydrogen bonds · protein-protein

Compared structures

5KOZ · Structure function studies of R. palustris RubisCO (K192C 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 5KOZ · PDBe 5KOZ · UniProt Q6N0W9

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