MolNFT v1 · #104811 · protein

Azurin mutant M121E with iron

4QLW: “Azurin mutant M121E with iron”. X-ray diffraction, 3 ligands (FE, NO3, SO4), 6 pockets (best druggability 0.75). MolNFT v1 #104811 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QLW
Type: protein
Length: 512 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Azurin
UniProt: P00282
Ligands: FE, NO3, SO4
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Azurin	protein	128	19% helix, 34% strand	P00282

Ligands and binding sites

FE · Fe (III) ion · metal · 2 copies · chains B, D
NO3 · Nitrate ion · ion · 10 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 3 copies · chains A, C

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	454	0.75	0.84	59	NO3
2	282	0.73	0.87	37	empty
3	70	0.70	0.96	19	empty
4	88	0.60	0.88	27	empty
5	143	0.41	0.74	27	empty

Interfaces

6 interfaces between chains.

A–D · 570 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 550 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 440 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 383 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 377 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4QLW · Azurin mutant M121E with iron · 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 B 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 P00282
Elsewhere: RCSB PDB 4QLW · PDBe 4QLW · UniProt P00282

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