MolNFT v1 · #104173 · protein

Inadl PDZ3 in complex with a phage-derived peptide

4Q2N · Inad-like protein: “Inadl PDZ3 in complex with a phage-derived peptide”. X-ray diffraction, 4 pockets (best druggability 0.76). MolNFT v1 #104173 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Q2N
Type: protein
Length: 572 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inad-like protein
UniProt: Q8NI35
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 6 distinct chains · 15% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Inad-like protein	protein	93	15% helix, 45% strand	Q8NI35
B	Inad-like protein	protein	99	14% helix, 42% strand	Q8NI35
C	Inad-like protein	protein	90	16% helix, 44% strand	Q8NI35
D	Inad-like protein	protein	95	15% helix, 46% strand	Q8NI35
E	Inad-like protein	protein	97	13% helix, 45% strand	Q8NI35
F	Inad-like protein	protein	98	15% helix, 45% strand	Q8NI35

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, E, F

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	885	0.76	0.79	100	empty
2	579	0.70	0.79	58	empty
3	134	0.68	0.89	28	empty
4	130	0.36	0.72	21	empty

Interfaces

6 interfaces between chains.

A–B · 1730 Å² buried · 37 hydrogen bonds · protein-protein
E–F · 1621 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 1586 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 309 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 247 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4Q2N · INADL PDZ3 in Complex with a Phage-Derived Peptide · the same entry in another collection · chain F against F, TM-score 1.00
Q8NI35 · AlphaFold monomer V2.0 prediction for inad-like protein (Q8NI35) · a predicted model of the same protein · chain E against A, TM-score 0.85

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 Q8NI35
Elsewhere: RCSB PDB 4Q2N · PDBe 4Q2N · UniProt Q8NI35

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