MolNFT v1 · #119457 · protein

Atomic cryoem structure of HSP90-CDC37-CDK4 complex

5FWM · Heat shock protein HSP 90 beta: “Atomic cryoem structure of HSP90-CDC37-CDK4 complex”. Electron microscopy, 2 ligands (ATP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #119457 on GenesisL1: 3D structure, binding sites and…

PDB: 5FWM
Type: protein
Length: 1,818 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock protein HSP 90 beta; HSP90 co-chaperone CDC37; Cyclin-dependent kinase 4
UniProt: P08238, Q16543, P11802
Ligands: ATP, MG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 4 distinct chains · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heat shock protein HSP 90 beta	protein	638	41% helix, 20% strand	P08238
B	Heat shock protein HSP 90 beta	protein	630	42% helix, 21% strand	P08238
E	HSP90 co-chaperone CDC37	protein	259	71% helix, 5% strand	Q16543
K	Cyclin-dependent kinase 4	protein	291	34% helix, 11% strand	P11802

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

20 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	902	0.83	0.85	99	empty
2	288	0.82	0.93	42	ATP
3	307	0.80	0.91	46	ATP, MG
4	765	0.79	0.83	96	empty
5	174	0.70	0.88	34	empty

Interfaces

6 interfaces between chains.

A–B · 4214 Å² buried · 53 hydrogen bonds · protein-protein
A–K · 2539 Å² buried · 46 hydrogen bonds · protein-protein
B–E · 2145 Å² buried · 43 hydrogen bonds · protein-protein
E–K · 1785 Å² buried · 24 hydrogen bonds · protein-protein
B–K · 1138 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

5FWM · Atomic cryoEM structure of Hsp90-Cdc37-Cdk4 complex · the same entry in another collection · chain K against K, TM-score 1.00
P08238 · AlphaFold monomer V2.0 prediction for heat shock protein HSP 90-beta (P08238) · a predicted model of the same protein · chain A against A, TM-score 0.96
P11802 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 4 (P11802) · a predicted model of the same protein · chain K against A, TM-score 0.63
Q16543 · AlphaFold monomer V2.0 prediction for HSP90 co-chaperone CDC37 (Q16543) · a predicted model of the same protein · chain E against A, TM-score 0.49

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 P08238
Every structure of UniProt Q16543
Every structure of UniProt P11802
Elsewhere: RCSB PDB 5FWM · PDBe 5FWM · UniProt P08238 · UniProt Q16543 · UniProt P11802

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