MolNFT v1 · #180302 · protein

Cryo-EM structure of mal de rio cuarto virus P9-1 viroplasm protein (dodecamer)

7KVD: “Cryo-EM structure of mal de rio cuarto virus P9-1 viroplasm protein (dodecamer)”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #180302 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KVD
Type: protein
Length: 3,192 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: P9-1
UniProt: D9U542
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 34% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	P9-1	protein	266	34% helix, 16% strand	D9U542

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	1106	0.85	0.86	170	empty
2	640	0.83	0.87	113	empty
3	1019	0.83	0.84	149	empty
4	1004	0.83	0.83	143	empty
5	721	0.82	0.86	109	empty

Interfaces

24 interfaces between chains.

F–G · 1411 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 1409 Å² buried · 10 hydrogen bonds · protein-protein
J–K · 1406 Å² buried · 10 hydrogen bonds · protein-protein
H–I · 1403 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 1399 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7KVD · Cryo-EM structure of Mal de Rio Cuarto virus P9-1 viroplasm protein (dodecamer) · 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 D9U542
Elsewhere: RCSB PDB 7KVD · PDBe 7KVD · UniProt D9U542

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