MolNFT v1 · #82107 · protein

Computationally designed self-assembling octahedral cage protein, O333, crystallized in space group R32

3VCD · Propanediol utilization polyhedral body protein pdut: “Computationally designed self-assembling octahedral cage protein, O333, crystallized in space group R32”. X-ray diffraction, 2 ligands (SO4, CL), 11 pockets (best druggability…

PDB: 3VCD
Type: protein
Length: 1,466 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Propanediol utilization polyhedral body protein pdut
UniProt: E7V033
Ligands: SO4, CL
Pockets: 11 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Propanediol utilization polyhedral body protein pdut	protein	184	41% helix, 36% strand	E7V033
B, C, D, F, G, H	Propanediol utilization polyhedral body protein pdut	protein	183	40% helix, 36% strand	E7V033

Ligands and binding sites

SO4 · Sulfate ion · ion · 26 copies · chains A, B, C, D, E, F, G, H
CL · Chloride ion · ion · chains H

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	134	0.53	0.81	35	empty
2	247	0.53	0.76	29	empty
3	246	0.50	0.75	30	empty
4	213	0.50	0.76	22	empty
5	99	0.50	0.82	29	empty

Interfaces

13 interfaces between chains.

A–C · 826 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 819 Å² buried · 12 hydrogen bonds · protein-protein
D–F · 813 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 812 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 809 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

3VCD · Computationally Designed Self-assembling Octahedral Cage protein, O333, Crystallized in… · 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 E7V033
Elsewhere: RCSB PDB 3VCD · PDBe 3VCD · UniProt E7V033

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