MolNFT v1 · #140999 · protein

Crystal structure of circularly permutated azurin 3

5YT7: “Crystal structure of circularly permutated azurin 3”. X-ray diffraction, 5 ligands (CU, CA, NA), 5 pockets (best druggability 0.69). MolNFT v1 #140999 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YT7
Type: protein
Length: 528 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Azurin
UniProt: P00282
Ligands: CU, CA, NA, NO3, CL
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Azurin	protein	133	18% helix, 34% strand	P00282
B	Azurin	protein	132	16% helix, 34% strand	P00282
C	Azurin	protein	130	16% helix, 35% strand	P00282

Ligands and binding sites

CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 3 copies · chains A, B
NA · Sodium ion · metal · 3 copies · chains A, C
NO3 · Nitrate ion · ion · 4 copies · chains A, B, D, C
CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

5 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	402	0.69	0.81	58	NA
2	315	0.53	0.75	39	empty
3	234	0.48	0.74	28	NO3
4	250	0.48	0.73	41	NO3
5	96	0.37	0.76	24	empty

Interfaces

4 interfaces between chains.

A–B · 450 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 319 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 307 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 120 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5YT7 · crystal structure of circularly permutated Azurin 3 · the same entry in another collection · chain D against D, TM-score 1.00
P00282 · AlphaFold monomer V2.0 prediction for azurin (P00282) · a predicted model of the same protein · chain C against A, TM-score 0.87

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 P00282
Elsewhere: RCSB PDB 5YT7 · PDBe 5YT7 · UniProt P00282

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