MolNFT v1 · #164075 · protein

Cryo-electron microscopy structure of a rbcl-RAF1 supercomplex from synechococcus elongatus pcc 7942

6SMH · Ribulose bisphosphate carboxylase large chain: “Cryo-electron microscopy structure of a rbcl-RAF1 supercomplex from synechococcus elongatus pcc 7942”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #164075 on…

PDB: 6SMH
Type: protein
Length: 5,025 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribulose bisphosphate carboxylase large chain; Rubisco accumulation factor 1 (RAF1)…
EC: 4.1.1.39
UniProt: Q31NB3, Q31Q05
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 6 distinct chains · 40% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39)	protein	447	36% helix, 13% strand	Q31NB3
I, K, L	Rubisco accumulation factor 1 (RAF1) peptide	protein	179	38% helix, 0% strand	Q31Q05
J	Rubisco accumulation factor 1 (RAF1) peptide	protein	188	37% helix, 0% strand	Q31Q05
M	Rubisco accumulation factor 1 (RAF1) peptide	protein	180	45% helix, 0% strand	Q31Q05
N, O	Rubisco accumulation factor 1 (RAF1) peptide	protein	181	46% helix, 0% strand	Q31Q05
P	Rubisco accumulation factor 1 (RAF1) peptide	protein	182	45% helix, 0% strand	Q31Q05

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	889	0.89	0.92	136	empty
2	967	0.88	0.89	129	empty
3	886	0.87	0.90	135	empty
4	890	0.87	0.89	115	empty
5	472	0.84	0.91	74	empty

Interfaces

40 interfaces between chains.

B–G · 3256 Å² buried · 40 hydrogen bonds · protein-protein
A–H · 3246 Å² buried · 29 hydrogen bonds · protein-protein
D–E · 3246 Å² buried · 29 hydrogen bonds · protein-protein
C–F · 3225 Å² buried · 31 hydrogen bonds · protein-protein
B–N · 1288 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

6SMH · Cryo-electron microscopy structure of a RbcL-Raf1 supercomplex from Synechococcus… · the same entry in another collection · chain P against P, 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 Q31NB3
Every structure of UniProt Q31Q05
Elsewhere: RCSB PDB 6SMH · PDBe 6SMH · UniProt Q31NB3 · UniProt Q31Q05

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