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Structure of the copper storage protein, ccsp, from streptomyces lividans loaded with 10 copper equivalents

Analyse Structure of the copper storage protein, ccsp, from streptomyces lividans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Q6B
Type: protein
Length: 483 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytosolic copper storage protein
UniProt: Q9X8F4
Ligands: CU1, CU
Pockets: 6 · best druggability 0.58

Structure

x-ray diffraction · 4 distinct chains · 82% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Cytosolic copper storage protein	protein	118	84% helix, 0% strand	Q9X8F4
C	Cytosolic copper storage protein	protein	116	84% helix, 0% strand	Q9X8F4
A	Cytosolic copper storage protein	protein	132	79% helix, 0% strand	Q9X8F4
D	Cytosolic copper storage protein	protein	117	83% helix, 0% strand	Q9X8F4

Ligands and binding sites

CU1 · Copper (I) ion · metal · 59 copies · chains B, C, A, D
CU · Copper (II) ion · metal · 5 copies · chains B, A, 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	226	0.58	0.79	37	empty
2	86	0.55	0.86	21	empty
3	158	0.49	0.78	23	empty
4	93	0.36	0.75	16	empty
5	64	0.32	0.75	15	empty

Interfaces

5 interfaces between chains.

C–A · 1070 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 695 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 524 Å² buried · 9 hydrogen bonds · protein-protein
B–A · 429 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 249 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6Q6B · Structure of the copper storage protein, Ccsp, from Streptomyces lividans loaded with 10… · 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 Q9X8F4
Elsewhere: RCSB PDB 6Q6B · PDBe 6Q6B · UniProt Q9X8F4

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