MolNFT v1 · #111799 · protein

Crystal structure of human TRAP1 with amppnp

4Z1I · Heat shock protein 75 kda, mitochondrial: “Crystal structure of human TRAP1 with amppnp”. X-ray diffraction, 2 ligands (ANP, MG), 20 pockets (best druggability 0.80). MolNFT v1 #111799 on GenesisL1: 3D structure, binding sites and…

PDB: 4Z1I
Type: protein
Length: 1,757 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat shock protein 75 kda, mitochondrial
UniProt: Q12931
Ligands: ANP, MG
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heat shock protein 75 kda, mitochondrial	protein	365	31% helix, 27% strand	Q12931
B	Heat shock protein 75 kda, mitochondrial	protein	472	36% helix, 25% strand	Q12931
C	Heat shock protein 75 kda, mitochondrial	protein	471	37% helix, 24% strand	Q12931
D	Heat shock protein 75 kda, mitochondrial	protein	449	34% helix, 26% strand	Q12931

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	263	0.80	0.92	41	ANP, MG
2	249	0.78	0.91	38	ANP, MG
3	267	0.78	0.90	40	ANP, MG
4	275	0.76	0.89	40	ANP, MG
5	65	0.75	0.99	19	empty

Interfaces

5 interfaces between chains.

B–D · 4029 Å² buried · 83 hydrogen bonds · protein-protein
A–C · 3481 Å² buried · 70 hydrogen bonds · protein-protein
B–C · 74 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 25 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 13 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent, 3 disulfide (covalent ligand, disulfide).

Compared structures

4Z1I · Crystal structure of human Trap1 with AMPPNP · the same entry in another collection · chain D against D, 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 D 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 4Z1I · PDBe 4Z1I · UniProt Q12931

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