MolNFT v1 · #34410 · protein

Crystal structure of infectious bursal disease virus VP2 subviral particle

2DF7 · Structural polyprotein VP2: “Crystal structure of infectious bursal disease virus VP2 subviral particle”. X-ray diffraction, 2 ligands (CA, CL), 20 pockets (best druggability 0.87). MolNFT v1 #34410 on GenesisL1: 3D structure…

PDB: 2DF7
Type: protein
Length: 8,290 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Structural polyprotein VP2
UniProt: Q6S9I7
Ligands: CA, CL
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 17 distinct chains · 13% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Structural polyprotein VP2	protein	420	14% helix, 46% strand	Q6S9I7
B	Structural polyprotein VP2	protein	418	13% helix, 45% strand	Q6S9I7
C, I	Structural polyprotein VP2	protein	413	14% helix, 48% strand	Q6S9I7
D	Structural polyprotein VP2	protein	413	14% helix, 47% strand	Q6S9I7
E	Structural polyprotein VP2	protein	415	14% helix, 48% strand	Q6S9I7
F	Structural polyprotein VP2	protein	413	13% helix, 48% strand	Q6S9I7
G, M	Structural polyprotein VP2	protein	412	13% helix, 49% strand	Q6S9I7
H	Structural polyprotein VP2	protein	413	14% helix, 48% strand	Q6S9I7
J	Structural polyprotein VP2	protein	411	14% helix, 48% strand	Q6S9I7
K	Structural polyprotein VP2	protein	417	13% helix, 48% strand	Q6S9I7
L, T	Structural polyprotein VP2	protein	418	13% helix, 48% strand	Q6S9I7
N	Structural polyprotein VP2	protein	413	13% helix, 47% strand	Q6S9I7
O	Structural polyprotein VP2	protein	412	14% helix, 49% strand	Q6S9I7
P	Structural polyprotein VP2	protein	417	13% helix, 46% strand	Q6S9I7
Q	Structural polyprotein VP2	protein	417	14% helix, 47% strand	Q6S9I7
R	Structural polyprotein VP2	protein	411	13% helix, 49% strand	Q6S9I7
S	Structural polyprotein VP2	protein	414	13% helix, 49% strand	Q6S9I7

Ligands and binding sites

CA · Calcium ion · metal · 8 copies · chains A, F, B, C, E, L, G, K, M, H, N, O, I, J, Q, P, R, S, T
CL · Chloride ion · ion · 8 copies · chains A, F, B, C, E, L, G, K, M, H, N, O, I, J, Q, P, R, S, T

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	432	0.87	0.95	42	empty
2	420	0.87	0.95	43	empty
3	424	0.87	0.95	43	empty
4	408	0.87	0.95	42	empty
5	1164	0.86	0.88	179	empty

Interfaces

43 interfaces between chains.

R–T · 2560 Å² buried · 48 hydrogen bonds · protein-protein
G–K · 2552 Å² buried · 43 hydrogen bonds · protein-protein
G–M · 2551 Å² buried · 45 hydrogen bonds · protein-protein
J–Q · 2547 Å² buried · 44 hydrogen bonds · protein-protein
I–J · 2546 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

2DF7 · Crystal structure of infectious bursal disease virus VP2 subviral particle · 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 Q6S9I7
Elsewhere: RCSB PDB 2DF7 · PDBe 2DF7 · UniProt Q6S9I7

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