MolNFT v1 · #122517 · protein

Crystal structure of rabbit NOD2 in an ADP-bound state (crystal FORM2)

5IRM · Uncharacterized protein: “Crystal structure of rabbit NOD2 in an ADP-bound state (crystal FORM2)”. X-ray diffraction, 1 ligand (ADP), 11 pockets (best druggability 0.84). MolNFT v1 #122517 on GenesisL1: 3D structure, binding sites…

PDB: 5IRM
Type: protein
Length: 1,537 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein
UniProt: G1T469
Ligands: ADP
Pockets: 11 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein	protein	767	51% helix, 11% strand	G1T469
C	Uncharacterized protein	protein	770	51% helix, 11% strand	G1T469

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	615	0.84	0.89	74	ADP
2	1058	0.83	0.84	122	empty
3	1045	0.81	0.82	79	ADP
4	557	0.78	0.85	68	empty
5	275	0.54	0.76	33	empty

Interfaces

1 interface between chains.

A–C · 1082 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5IRM · Crystal structure of rabbit NOD2 in an ADP-bound state (Crystal form2) · 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 G1T469
Elsewhere: RCSB PDB 5IRM · PDBe 5IRM · UniProt G1T469

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