MolNFT v1 · #116044 · protein

Isdb NEAT2 bound by clone D2-06

5D1Q · D2-06 light chain: “Isdb NEAT2 bound by clone D2-06”. X-ray diffraction, 10 pockets (best druggability 0.66). MolNFT v1 #116044 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5D1Q
Type: protein
Length: 993 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D2-06 light chain; D2-06 heavy chain; P5 heavy chain; P5 light chain; Iron-regulated…
UniProt: Q2YX96
Pockets: 10 · best druggability 0.66

Structure

x-ray diffraction · 5 distinct chains · 5% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D2-06 light chain	protein	214	5% helix, 49% strand	—
B	D2-06 heavy chain	protein	216	4% helix, 48% strand	—
C	P5 heavy chain	protein	231	5% helix, 48% strand	—
D	P5 light chain	protein	214	5% helix, 51% strand	—
E	Iron-regulated surface determinant protein B	protein	118	9% helix, 60% strand	Q2YX96

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	687	0.66	0.75	72	empty
2	243	0.57	0.78	34	empty
3	344	0.54	0.74	47	empty
4	65	0.54	0.87	21	empty
5	326	0.53	0.74	50	empty

Interfaces

7 interfaces between chains.

C–D · 2045 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1897 Å² buried · 18 hydrogen bonds · protein-protein
B–E · 700 Å² buried · 13 hydrogen bonds · protein-protein
C–E · 454 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 339 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5D1Q · IsdB NEAT2 bound by clone D2-06 · the same entry in another collection · chain A against A, TM-score 1.00
Q2YX96 · AlphaFold monomer V2.0 prediction for iron-regulated surface determinant protein B… · a predicted model of the same protein · chain E against A, TM-score 0.96

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 Q2YX96
Elsewhere: RCSB PDB 5D1Q · PDBe 5D1Q · UniProt Q2YX96

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