MolNFT v1 · #154730 · protein

Crystal structure of rbcl-RAF1 complex from anabaena sp. pcc 7120

6KKM · ALL5250 protein: “Crystal structure of rbcl-RAF1 complex from anabaena sp. pcc 7120”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #154730 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KKM
Type: protein
Length: 3,121 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ALL5250 protein; Ribulose bisphosphate carboxylase large chain
EC: 4.1.1.39
UniProt: Q8YLP6, P00879
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 7 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	ALL5250 protein	protein	334	41% helix, 16% strand	Q8YLP6
F	ALL5250 protein	protein	333	41% helix, 16% strand	Q8YLP6
G	ALL5250 protein	protein	329	41% helix, 15% strand	Q8YLP6
H	ALL5250 protein	protein	332	40% helix, 16% strand	Q8YLP6
A	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39)	protein	451	43% helix, 18% strand	P00879
B, D	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39)	protein	445	42% helix, 18% strand	P00879
C	Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39)	protein	452	40% helix, 18% strand	P00879

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	1111	0.88	0.89	133	empty
2	945	0.86	0.88	88	empty
3	972	0.84	0.86	92	empty
4	781	0.83	0.86	78	empty
5	204	0.82	0.96	41	empty

Interfaces

19 interfaces between chains.

C–D · 3605 Å² buried · 51 hydrogen bonds · protein-protein
A–B · 3515 Å² buried · 51 hydrogen bonds · protein-protein
E–F · 3141 Å² buried · 31 hydrogen bonds · protein-protein
G–H · 2755 Å² buried · 29 hydrogen bonds · protein-protein
E–A · 1754 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6KKM · Crystal structure of RbcL-Raf1 complex from Anabaena sp. PCC 7120 · the same entry in another collection · chain D against D, TM-score 1.00
P00879 · AlphaFold monomer V2.0 prediction for ribulose bisphosphate carboxylase large chain… · a predicted model of the same protein · chain B against A, TM-score 0.97
Q8YLP6 · AlphaFold monomer V2.0 prediction for rubisco accumulation factor 1 (Q8YLP6) · a predicted model of the same protein · chain H against A, TM-score 0.61

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 Q8YLP6
Every structure of UniProt P00879
Elsewhere: RCSB PDB 6KKM · PDBe 6KKM · UniProt Q8YLP6 · UniProt P00879

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