MolNFT v1 · #105456 · protein

Crystal structure of the dnak C-terminus (dnak-sbd-a)

4R5J · Chaperone protein dnak: “Crystal structure of the dnak C-terminus (dnak-sbd-a)”. X-ray diffraction, 2 ligands (CA, PO4), 7 pockets (best druggability 0.76). MolNFT v1 #105456 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4R5J
Type: protein
Length: 881 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone protein dnak
UniProt: P0A6Y8
Ligands: CA, PO4
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone protein dnak	protein	218	39% helix, 29% strand	P0A6Y8
B	Chaperone protein dnak	protein	218	39% helix, 26% strand	P0A6Y8
C	Chaperone protein dnak	protein	224	39% helix, 28% strand	P0A6Y8
D	Chaperone protein dnak	protein	221	39% helix, 27% strand	P0A6Y8

Ligands and binding sites

CA · Calcium ion · metal · 5 copies · chains A, C, B, D
PO4 · Phosphate ion · ion · 2 copies · chains C, D

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1098	0.76	0.79	118	CA
2	725	0.74	0.79	87	empty
3	117	0.55	0.83	21	PO4
4	130	0.53	0.81	20	PO4
5	167	0.52	0.78	24	empty

Interfaces

5 interfaces between chains.

A–C · 1748 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 441 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 217 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 139 Å² buried · 1 hydrogen bond · protein-protein
A–D · 23 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4R5J · Crystal structure of the DnaK C-terminus (Dnak-SBD-A) · the same entry in another collection · chain D against D, TM-score 1.00
P0A6Y8 · AlphaFold monomer V2.0 prediction for chaperone protein dnak (P0A6Y8) · a predicted model of the same protein · chain B against A, TM-score 0.47

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 P0A6Y8
Elsewhere: RCSB PDB 4R5J · PDBe 4R5J · UniProt P0A6Y8

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