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Isdb NEAT2 bound by D4-30

Analyse Isdb NEAT2 bound by D4-30 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5D1X
Type: protein
Length: 869 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D4-30 light chain; D4-30 heavy chain; P5 heavy chain; P5 light chain; Iron-regulated…
UniProt: Q2FHV2
Pockets: 9 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 6% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D4-30 light chain	protein	218	5% helix, 50% strand	—
B	D4-30 heavy chain	protein	212	6% helix, 50% strand	—
C	P5 heavy chain	protein	127	2% helix, 38% strand	—
D	P5 light chain	protein	197	8% helix, 35% strand	—
E	Iron-regulated surface determinant protein B	protein	115	6% helix, 60% strand	Q2FHV2

Pockets

9 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	788	0.70	0.77	75	empty
2	118	0.53	0.82	21	empty
3	318	0.52	0.74	52	empty
4	224	0.46	0.74	35	empty
5	107	0.44	0.78	23	empty

Interfaces

6 interfaces between chains.

A–B · 1761 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1072 Å² buried · 6 hydrogen bonds · protein-protein
B–E · 667 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 423 Å² buried · 6 hydrogen bonds · protein-protein
D–E · 318 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

5D1X · IsdB NEAT2 bound by D4-30 · the same entry in another collection · chain A against A, TM-score 1.00
Q2FHV2 · 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 0.95

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 Q2FHV2
Elsewhere: RCSB PDB 5D1X · PDBe 5D1X · UniProt Q2FHV2

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