MolNFT v1 · #18435 · protein

Volvatoxin A2 in monoclinic crystal

1PP0: “Volvatoxin A2 in monoclinic crystal”. X-ray diffraction, 11 pockets (best druggability 0.75). MolNFT v1 #18435 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PP0
Type: protein
Length: 770 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Volvatoxin A2
UniProt: Q6USC4
Pockets: 11 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Volvatoxin A2	protein	191	31% helix, 40% strand	Q6USC4
B, C	Volvatoxin A2	protein	194	30% helix, 40% strand	Q6USC4

Ligands and binding sites

ACY · Acetic acid · additive · 13 copies · chains A, B, D, C

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

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1052	0.75	0.78	100	empty
2	85	0.54	0.85	15	ACY
3	242	0.51	0.75	23	empty
4	164	0.49	0.77	29	ACY
5	238	0.47	0.73	39	ACY

Interfaces

4 interfaces between chains.

C–D · 647 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 626 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 407 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 374 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1PP0 · volvatoxin A2 in monoclinic crystal · 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 Q6USC4
Elsewhere: RCSB PDB 1PP0 · PDBe 1PP0 · UniProt Q6USC4

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