MolNFT v1 · #120857 · protein

Crystal structure of heat shock factor 2-dbd

5HDK · Heat shock factor protein 2: “Crystal structure of heat shock factor 2-dbd”. X-ray diffraction, 3 ligands (NA, K, CL), 6 pockets (best druggability 0.54). MolNFT v1 #120857 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5HDK
Type: protein
Length: 400 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock factor protein 2
UniProt: Q03933
Ligands: NA, K, CL
Pockets: 6 · best druggability 0.54

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heat shock factor protein 2	protein	99	42% helix, 16% strand	Q03933
B	Heat shock factor protein 2	protein	97	43% helix, 13% strand	Q03933
C	Heat shock factor protein 2	protein	96	45% helix, 15% strand	Q03933
D	Heat shock factor protein 2	protein	108	39% helix, 12% strand	Q03933

Ligands and binding sites

NA · Sodium ion · metal · 9 copies · chains A, B, C, D
K · Potassium ion · metal · 6 copies · chains A, B, C, D
CL · Chloride ion · ion · 3 copies · chains B, D

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	225	0.54	0.77	22	empty
2	102	0.50	0.82	29	NA
3	174	0.45	0.75	19	empty
4	181	0.42	0.73	23	empty
5	149	0.40	0.73	21	empty

Interfaces

4 interfaces between chains.

A–D · 566 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 537 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 307 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 188 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5HDK · Crystal structure of heat shock factor 2-DBD · the same entry in another collection · chain D against D, TM-score 1.00
Q03933 · AlphaFold monomer V2.0 prediction for heat shock factor protein 2 (Q03933) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q03933
Elsewhere: RCSB PDB 5HDK · PDBe 5HDK · UniProt Q03933

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