MolNFT v1 · #68174 · protein

Atomic model of cytoplasmic polyhedrosis virus with SAM and GTP

3JB2 · Structural protein VP3: “Atomic model of cytoplasmic polyhedrosis virus with SAM and GTP”. Electron microscopy, 3 ligands (SAM, GTP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #68174 on GenesisL1: 3D structure, binding…

PDB: 3JB2
Type: protein
Length: 4,083 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Structural protein VP3; Capsid protein VP1; Viral structural protein 5
UniProt: Q914N6, Q6TS43, C6K2M8
Ligands: SAM, GTP, MG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 4 distinct chains · 35% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Structural protein VP3	protein	1057	37% helix, 17% strand	Q914N6
B	Capsid protein VP1	protein	1191	35% helix, 17% strand	Q6TS43
C	Capsid protein VP1	protein	1251	33% helix, 18% strand	Q6TS43
D, E	Viral structural protein 5	protein	292	43% helix, 18% strand	C6K2M8

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A
GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A
MG · Magnesium ion · metal · chains A

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	518	0.85	0.91	46	empty
2	1059	0.84	0.85	104	empty
3	725	0.84	0.87	60	empty
4	926	0.82	0.84	101	empty
5	854	0.80	0.83	82	empty

Interfaces

6 interfaces between chains.

B–C · 3431 Å² buried · 52 hydrogen bonds · protein-protein
B–D · 2323 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 2023 Å² buried · 22 hydrogen bonds · protein-protein
C–E · 1048 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 832 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3JB2 · Atomic model of cytoplasmic polyhedrosis virus with SAM and GTP · 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 Q914N6
Every structure of UniProt Q6TS43
Every structure of UniProt C6K2M8
Elsewhere: RCSB PDB 3JB2 · PDBe 3JB2 · UniProt Q914N6 · UniProt Q6TS43 · UniProt C6K2M8

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