MolNFT v1 · #108355 · protein

Anti-marburgvirus nucleoprotein single domain antibody B complexed with nucleoprotein C-terminal domain

4W2O: “Anti-marburgvirus nucleoprotein single domain antibody B complexed with nucleoprotein C-terminal domain”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.68). MolNFT v1 #108355 on GenesisL1: 3D structure, binding…

PDB: 4W2O
Type: protein
Length: 728 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-marburgvirus nucleoprotein single domain antibody B; Nucleoprotein
UniProt: P27588
Ligands: SO4
Pockets: 5 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Anti-marburgvirus nucleoprotein single domain antibody B	protein	118	3% helix, 52% strand	—
B, D, F, H	Nucleoprotein	protein	64	56% helix, 13% strand	P27588

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, C, D, B, E, G, H

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

Pockets

5 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	351	0.68	0.81	32	SO4
2	584	0.63	0.74	44	SO4
3	151	0.50	0.78	31	empty
4	161	0.49	0.77	32	empty
5	189	0.47	0.75	26	empty

Interfaces

14 interfaces between chains.

C–D · 708 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 691 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 687 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 675 Å² buried · 10 hydrogen bonds · protein-protein
B–H · 430 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4W2O · Anti-Marburgvirus Nucleoprotein Single Domain Antibody B Complexed with Nucleoprotein… · 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 P27588
Elsewhere: RCSB PDB 4W2O · PDBe 4W2O · UniProt P27588

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