MolNFT v1 · #158575 · protein

Structure of a MAPK pathway complex

6NYB · SERINE/THREONINE-protein kinase B-RAF: “Structure of a MAPK pathway complex”. Electron microscopy, 5 ligands (AGS, ADP, LCJ), 13 pockets (best druggability 0.82). MolNFT v1 #158575 on GenesisL1: 3D structure, binding sites and…

PDB: 6NYB
Type: protein
Length: 1,097 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase B-RAF; Dual specificity mitogen-activated protein kinase…
EC: 2.7.11.1, 2.7.12.2
UniProt: P15056, Q02750, V9P4T4
Ligands: AGS, ADP, LCJ, ZN, MG
Pockets: 13 · best druggability 0.82

Structure

electron microscopy · 3 distinct chains · 46% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1)	protein	350	29% helix, 14% strand	P15056
B	Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2)	protein	289	44% helix, 17% strand	Q02750
C, D	14-3-3 protein zeta	protein	229	77% helix, 0% strand	V9P4T4

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · chains A
ADP · Adenosine-5'-diphosphate · ligand · chains B
LCJ · 5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy) imidazo[1,5-a]pyridine-6-carboxamide · ligand · chains B
ZN · Zinc ion · metal · 2 copies · chains A
MG · Magnesium ion · metal · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	709	0.82	0.86	77	empty
2	726	0.82	0.86	71	ADP, MG, LCJ
3	425	0.80	0.89	51	empty
4	865	0.77	0.80	80	AGS
5	253	0.72	0.87	37	empty

Interfaces

4 interfaces between chains.

A–C · 1638 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 1329 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1304 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1064 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

6NYB · Structure of a MAPK pathway complex · the same entry in another collection · chain A against A, TM-score 1.00
P15056 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase B-RAF (P15056) · a predicted model of the same protein · chain A against A, TM-score 0.75

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 P15056
Every structure of UniProt Q02750
Every structure of UniProt V9P4T4
Elsewhere: RCSB PDB 6NYB · PDBe 6NYB · UniProt P15056 · UniProt Q02750 · UniProt V9P4T4

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