MolNFT v1 · #116053 · protein

Isdb NEAT1 bound by clone D4-10

5D1Z · Y10 light chain: “Isdb NEAT1 bound by clone D4-10”. X-ray diffraction, 20 pockets (best druggability 0.68). MolNFT v1 #116053 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5D1Z
Type: protein
Length: 2,039 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Y10 light chain; Y10 heavy chain; D4-10 light chain; D4-10 heavy chain; Iron-regulated…
UniProt: Q6GA86
Pockets: 20 · best druggability 0.68

Structure

x-ray diffraction · 9 distinct chains · 5% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Y10 light chain	protein	213	5% helix, 48% strand	—
B	Y10 heavy chain	protein	218	1% helix, 49% strand	—
C	D4-10 light chain	protein	208	4% helix, 46% strand	—
D	D4-10 heavy chain	protein	230	3% helix, 43% strand	—
I, J	Iron-regulated surface determinant protein B	protein	149	10% helix, 44% strand	Q6GA86
E	D4-10 light chain	protein	213	5% helix, 46% strand	—
F	D4-10 heavy chain	protein	223	5% helix, 42% strand	—
G	Y10 heavy chain	protein	222	4% helix, 50% strand	—
H	Y10 light chain	protein	214	6% helix, 47% strand	—

Pockets

20 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	744	0.68	0.76	74	empty
2	651	0.65	0.75	63	empty
3	540	0.64	0.76	38	empty
4	484	0.61	0.75	60	empty
5	340	0.56	0.76	39	empty

Interfaces

19 interfaces between chains.

G–H · 1997 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 1944 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1942 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1863 Å² buried · 15 hydrogen bonds · protein-protein
F–J · 708 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 disulfide (disulfide).

Compared structures

5D1Z · IsdB NEAT1 bound by clone D4-10 · the same entry in another collection · chain J against J, TM-score 1.00
Q6GA86 · AlphaFold monomer V2.0 prediction for iron-regulated surface determinant protein B… · a predicted model of the same protein · chain I against A, TM-score 0.97

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 Q6GA86
Elsewhere: RCSB PDB 5D1Z · PDBe 5D1Z · UniProt Q6GA86

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