MolNFT v1 · #151314 · protein

X-ray structure of a truncated mutant of the metallochaperone cooj with a high-affinity nickel-binding site

6HK5: “X-ray structure of a truncated mutant of the metallochaperone cooj with a high-affinity nickel-binding site”. X-ray diffraction, 4 ligands (Z3P, NI, CA), 3 pockets (best druggability 0.81). MolNFT v1 #151314 on GenesisL1: 3D…

PDB: 6HK5
Type: protein
Length: 509 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cooj
UniProt: P72321
Ligands: Z3P, NI, CA, CL
Pockets: 3 · best druggability 0.81

Structure

x-ray diffraction · 7 distinct chains · 88% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, G	Cooj	protein	66	86% helix, 0% strand	P72321
C	Cooj	protein	63	90% helix, 0% strand	P72321
E	Cooj	protein	64	89% helix, 0% strand	P72321
A	Cooj	protein	65	88% helix, 0% strand	P72321
D	Cooj	protein	64	86% helix, 0% strand	P72321
F	Cooj	protein	61	90% helix, 0% strand	P72321
H	Cooj	protein	60	85% helix, 0% strand	P72321

Ligands and binding sites

Z3P · 3,3',3''-phosphoryltripropanoic acid · ligand · chains C, D, F
NI · Nickel (II) ion · metal · 4 copies · chains B, C, G, E, A, D, F, H
CA · Calcium ion · metal · chains C, G, D
CL · Chloride ion · ion · 3 copies · chains C, B
PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B, A, F, H, D
PGE · Triethylene glycol · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	623	0.81	0.86	69	CA, PEG, Z3P
2	275	0.73	0.87	35	empty
3	545	0.72	0.81	55	empty

Interfaces

17 interfaces between chains.

B–C · 1560 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 1531 Å² buried · 11 hydrogen bonds · protein-protein
E–G · 1478 Å² buried · 9 hydrogen bonds · protein-protein
F–H · 1476 Å² buried · 11 hydrogen bonds · protein-protein
C–F · 561 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

6HK5 · X-ray structure of a truncated mutant of the metallochaperone CooJ with a high-affinity… · the same entry in another collection · chain B against B, TM-score 1.00

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 P72321
Elsewhere: RCSB PDB 6HK5 · PDBe 6HK5 · UniProt P72321

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