MolNFT v1 · #58605 · protein

Fragment of wzzb, polysaccharide co-polymerase from salmonella typhimurium

3B8P · Chain length determinant protein: “Fragment of wzzb, polysaccharide co-polymerase from salmonella typhimurium”. X-ray diffraction, 14 pockets (best druggability 0.71). MolNFT v1 #58605 on GenesisL1: 3D structure, binding sites and…

PDB: 3B8P
Type: protein
Length: 940 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chain length determinant protein
UniProt: Q04866
Pockets: 14 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 54% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chain length determinant protein	protein	207	56% helix, 12% strand	Q04866
B	Chain length determinant protein	protein	174	52% helix, 14% strand	Q04866
C	Chain length determinant protein	protein	185	52% helix, 13% strand	Q04866
D	Chain length determinant protein	protein	185	53% helix, 13% strand	Q04866
E	Chain length determinant protein	protein	189	54% helix, 13% strand	Q04866

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1023	0.71	0.75	93	empty
2	580	0.66	0.76	60	empty
3	600	0.63	0.74	53	empty
4	416	0.62	0.77	39	empty
5	178	0.49	0.77	30	empty

Interfaces

5 interfaces between chains.

A–C · 629 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 622 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 622 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 619 Å² buried · 8 hydrogen bonds · protein-protein
C–E · 592 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (engineered).

Compared structures

3B8P · Fragment of WzzB, Polysaccharide Co-polymerase from Salmonella Typhimurium · the same entry in another collection · chain E against E, TM-score 1.00
Q04866 · AlphaFold monomer V2.0 prediction for chain length determinant protein (Q04866) · a predicted model of the same protein · chain D against A, TM-score 0.97

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 Q04866
Elsewhere: RCSB PDB 3B8P · PDBe 3B8P · UniProt Q04866

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