MolNFT v1 · #171045 · protein

VIP3BC1 tetramer

6YRF · Vegetative insecticidal protein: “VIP3BC1 tetramer”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #171045 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YRF
Type: protein
Length: 3,108 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vegetative insecticidal protein
UniProt: A0A290WPI2
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Vegetative insecticidal protein	protein	777	30% helix, 27% strand	A0A290WPI2

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1182	0.83	0.84	103	empty
2	104	0.78	0.97	25	empty
3	480	0.75	0.84	65	empty
4	85	0.75	0.96	24	empty
5	88	0.73	0.95	25	empty

Interfaces

6 interfaces between chains.

A–B · 2753 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 2751 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1203 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 1198 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 687 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6YRF · Vip3Bc1 tetramer · 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 A0A290WPI2
Elsewhere: RCSB PDB 6YRF · PDBe 6YRF · UniProt A0A290WPI2

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