MolNFT v1 · #134917 · protein

Structure of WWP2 WW2-2,3-linker-hect aa 334-398 linked to 485-865

5TJ7 · NEDD4-like E3 ubiquitin-protein ligase WWP2: “Structure of WWP2 WW2-2,3-linker-hect aa 334-398 linked to 485-865”. X-ray diffraction, 3 ligands (NA, SCN, CL), 20 pockets (best druggability 0.88). MolNFT v1 #134917 on GenesisL1: 3D…

PDB: 5TJ7
Type: protein
Length: 1,761 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NEDD4-like E3 ubiquitin-protein ligase WWP2
EC: 2.3.2.26
UniProt: O00308
Ligands: NA, SCN, CL
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NEDD4-like E3 ubiquitin-protein ligase WWP2 (EC 2.3.2.26)	protein	436	45% helix, 14% strand	O00308
B, D	NEDD4-like E3 ubiquitin-protein ligase WWP2 (EC 2.3.2.26)	protein	445	46% helix, 13% strand	O00308
C	NEDD4-like E3 ubiquitin-protein ligase WWP2 (EC 2.3.2.26)	protein	435	44% helix, 14% strand	O00308

Ligands and binding sites

NA · Sodium ion · metal · 3 copies · chains A, B, D
SCN · Thiocyanate ion · ion · chains C
CL · Chloride ion · ion · chains D

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1012	0.88	0.89	92	empty
2	655	0.81	0.86	85	empty
3	1011	0.78	0.80	81	empty
4	526	0.76	0.83	67	empty
5	71	0.75	0.99	15	empty

Interfaces

5 interfaces between chains.

B–C · 1433 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 590 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 584 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 453 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 369 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5TJ7 · Structure of WWP2 WW2-2,3-linker-HECT aa 334-398 linked to 485-865 · the same entry in another collection · chain A against A, TM-score 1.00
O00308 · AlphaFold monomer V2.0 prediction for NEDD4-like E3 ubiquitin-protein ligase WWP2 (O00308) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 O00308
Elsewhere: RCSB PDB 5TJ7 · PDBe 5TJ7 · UniProt O00308

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