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Structure of vaccinia virus D8 protein bound to human Fab VV138

Analyse Structure of vaccinia virus D8 protein bound to human Fab VV138 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B9J
Type: protein
Length: 1,302 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Imv membrane protein; Fab VV138 heavy chain; Fab VV138 light chain
UniProt: Q1M1K6
Ligands: NA
Pockets: 18 · best druggability 0.63

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X, Y	Imv membrane protein	protein	228	10% helix, 40% strand	Q1M1K6
H, A	Fab VV138 heavy chain	protein	212	6% helix, 51% strand	—
L	Fab VV138 light chain	protein	209	6% helix, 47% strand	—
B	Fab VV138 light chain	protein	213	6% helix, 50% strand	—

Ligands and binding sites

NA · Sodium ion · metal · 7 copies · chains X, H, L, Y
GOL · Glycerol · additive · 2 copies · chains X, Y

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

Pockets

18 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	176	0.63	0.84	29	empty
2	183	0.63	0.84	34	empty
3	332	0.63	0.79	46	empty
4	331	0.53	0.74	46	empty
5	224	0.52	0.76	23	empty

Interfaces

7 interfaces between chains.

H–L · 1718 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1555 Å² buried · 8 hydrogen bonds · protein-protein
Y–A · 767 Å² buried · 21 hydrogen bonds · protein-protein
X–H · 745 Å² buried · 19 hydrogen bonds · protein-protein
X–Y · 329 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6B9J · Structure of vaccinia virus D8 protein bound to human Fab vv138 · the same entry in another collection · chain B against B, 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 Q1M1K6
Elsewhere: RCSB PDB 6B9J · PDBe 6B9J · UniProt Q1M1K6

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