MolNFT v1 · #160998 · protein

Structure of a MAPK pathway complex

6Q0J · SERINE/THREONINE-protein kinase B-RAF: “Structure of a MAPK pathway complex”. Electron microscopy, 3 ligands (LCJ, AGS, MG), 18 pockets (best druggability 0.83). MolNFT v1 #160998 on GenesisL1: 3D structure, binding sites and…

PDB: 6Q0J
Type: protein
Length: 1,633 residues
Chains: 6
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: LCJ, AGS, MG
Pockets: 18 · best druggability 0.83

Structure

electron microscopy · 4 distinct chains · 48% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1)	protein	281	38% helix, 14% strand	P15056
B	SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1)	protein	282	38% helix, 14% strand	P15056
C, D	Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.12.2)	protein	306	47% helix, 16% strand	Q02750
X, Y	14-3-3 protein zeta	protein	229	74% helix, 0% strand	V9P4T4

Ligands and binding sites

LCJ · 5-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy) imidazo[1,5-a]pyridine-6-carboxamide · ligand · 2 copies · chains C, D
AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains C, D
MG · Magnesium ion · metal · 2 copies · chains C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	948	0.83	0.84	123	LCJ
2	983	0.82	0.84	150	empty
3	476	0.78	0.86	91	empty
4	1097	0.75	0.78	142	empty
5	1071	0.75	0.77	143	empty

Interfaces

6 interfaces between chains.

A–C · 305 Å² buried · 0 hydrogen bonds · protein-protein
A–X · 288 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 276 Å² buried · 0 hydrogen bonds · protein-protein
B–Y · 269 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 116 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

6Q0J · Structure of a MAPK pathway complex · the same entry in another collection · chain Y against Y, 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 0.92

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 6Q0J · PDBe 6Q0J · UniProt P15056 · UniProt Q02750 · UniProt V9P4T4

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