MolNFT v1 · #110572 · protein

Yeaz from pseudomonas aeruginosa

4Y0W: “Yeaz from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (NA), 9 pockets (best druggability 0.83). MolNFT v1 #110572 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Y0W
Type: protein
Length: 1,053 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yeaz
UniProt: K0Y2M1
Ligands: NA
Pockets: 9 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 35% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yeaz	protein	215	33% helix, 28% strand	K0Y2M1
B	Yeaz	protein	212	36% helix, 29% strand	K0Y2M1
C	Yeaz	protein	213	36% helix, 28% strand	K0Y2M1
D	Yeaz	protein	205	36% helix, 29% strand	K0Y2M1
E	Yeaz	protein	208	37% helix, 28% strand	K0Y2M1

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A, B, C

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

Pockets

9 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	777	0.83	0.86	93	empty
2	641	0.80	0.84	76	empty
3	401	0.76	0.85	43	empty
4	256	0.68	0.84	40	empty
5	148	0.50	0.78	23	empty

Interfaces

9 interfaces between chains.

A–D · 1118 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 1100 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 764 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 588 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 526 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4Y0W · YeaZ from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, 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 K0Y2M1
Elsewhere: RCSB PDB 4Y0W · PDBe 4Y0W · UniProt K0Y2M1

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