MolNFT v1 · #116436 · protein

Crystal structure of recombinant foot-and-mouth-disease virus O1M- S2093Y empty capsid

5DDJ · Foot and mouth disease virus, VP1: “Crystal structure of recombinant foot-and-mouth-disease virus O1M- S2093Y empty capsid”. X-ray diffraction, 9 pockets (best druggability 0.77). MolNFT v1 #116436 on GenesisL1: 3D structure…

PDB: 5DDJ
Type: protein
Length: 660 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Foot and mouth disease virus, VP1; Foot and mouth disease virus, VP2; Foot and mouth…
UniProt: Q6PMW3
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Foot and mouth disease virus, VP1	protein	184	11% helix, 20% strand	Q6PMW3
2	Foot and mouth disease virus, VP2	protein	210	7% helix, 30% strand	Q6PMW3
3	Foot and mouth disease virus, VP3	protein	220	6% helix, 20% strand	Q6PMW3
4	Genome polyprotein	protein	46	7% helix, 0% strand	Q6PMW3

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	947	0.77	0.79	95	empty
2	80	0.74	0.96	24	empty
3	461	0.70	0.80	56	empty
4	303	0.61	0.79	40	empty
5	146	0.48	0.78	19	empty

Interfaces

6 interfaces between chains.

1–2 · 1275 Å² buried · 16 hydrogen bonds · protein-protein
1–3 · 971 Å² buried · 17 hydrogen bonds · protein-protein
2–3 · 969 Å² buried · 16 hydrogen bonds · protein-protein
1–4 · 909 Å² buried · 15 hydrogen bonds · protein-protein
2–4 · 257 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5DDJ · Crystal structure of recombinant foot-and-mouth-disease virus O1M-S2093Y empty capsid · the same entry in another collection · chain 1 against 1, 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 Q6PMW3
Elsewhere: RCSB PDB 5DDJ · PDBe 5DDJ · UniProt Q6PMW3

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