MolNFT v1 · #76958 · protein

Structure of inad PDZ45 in complex with NG2 peptide

3R0H · Inactivation-no-after-potential D protein: “Structure of inad PDZ45 in complex with NG2 peptide”. X-ray diffraction, 2 ligands (DTV, SO4), 20 pockets (best druggability 0.83). MolNFT v1 #76958 on GenesisL1: 3D structure, binding…

PDB: 3R0H
Type: protein
Length: 1,646 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inactivation-no-after-potential D protein; NG2
UniProt: Q24008
Ligands: DTV, SO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 7 distinct chains · 15% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Inactivation-no-after-potential D protein	protein	198	16% helix, 33% strand	Q24008
a, b, c, d, e, f, g, h	NG2	protein	9	0% helix, 44% strand	—
B	Inactivation-no-after-potential D protein	protein	196	16% helix, 35% strand	Q24008
C	Inactivation-no-after-potential D protein	protein	198	15% helix, 34% strand	Q24008
D	Inactivation-no-after-potential D protein	protein	199	16% helix, 35% strand	Q24008
E	Inactivation-no-after-potential D protein	protein	199	15% helix, 35% strand	Q24008
G, H	Inactivation-no-after-potential D protein	protein	193	15% helix, 34% strand	Q24008

Ligands and binding sites

DTV · (2S,3S)-1,4-dimercaptobutane-2,3-diol · ligand · chains A, B, C, D
SO4 · Sulfate ion · ion · 5 copies · chains C, D, G, H
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 4 copies · chains A, a, D, B, b, C, 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, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1058	0.83	0.84	83	SO4
2	1113	0.83	0.84	83	SO4
3	423	0.80	0.88	71	empty
4	229	0.72	0.88	40	DTV
5	211	0.69	0.86	36	empty

Interfaces

36 interfaces between chains.

A–B · 604 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 603 Å² buried · 3 hydrogen bonds · protein-protein
G–g · 512 Å² buried · 11 hydrogen bonds · protein-protein
H–h · 490 Å² buried · 10 hydrogen bonds · protein-protein
C–c · 487 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3R0H · Structure of INAD PDZ45 in complex with NG2 peptide · the same entry in another collection · chain h against h, 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 Q24008
Elsewhere: RCSB PDB 3R0H · PDBe 3R0H · UniProt Q24008

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