MolNFT v1 · #121243 · protein

Structure of TRAP1 fragment

5HPH · Heat shock protein 75 kda, mitochondrial: “Structure of TRAP1 fragment”. X-ray diffraction, 4 ligands (ANP, MG, PO4), 16 pockets (best druggability 0.78). MolNFT v1 #121243 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5HPH
Type: protein
Length: 965 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock protein 75 kda, mitochondrial
UniProt: Q12931
Ligands: ANP, MG, PO4, SO4
Pockets: 16 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heat shock protein 75 kda, mitochondrial	protein	482	36% helix, 24% strand	Q12931
B	Heat shock protein 75 kda, mitochondrial	protein	483	38% helix, 24% strand	Q12931

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 3 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	256	0.78	0.91	39	ANP, MG
2	269	0.78	0.90	39	ANP, MG
3	65	0.76	0.99	15	empty
4	571	0.66	0.77	68	empty
5	264	0.60	0.79	43	PO4

Interfaces

1 interface between chains.

A–B · 4040 Å² buried · 69 hydrogen bonds · protein-protein

Compared structures

5HPH · Structure of TRAP1 fragment · the same entry in another collection · chain A against A, TM-score 1.00
Q12931 · AlphaFold monomer V2.0 prediction for heat shock protein 75 kda, mitochondrial (Q12931) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q12931
Elsewhere: RCSB PDB 5HPH · PDBe 5HPH · UniProt Q12931

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