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Structure of POMBC5, a periplasmic fragment of pomb from vibrio

Analyse Structure of POMBC5, a periplasmic fragment of pomb from vibrio in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WPW
Type: protein
Length: 298 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pomb
UniProt: O06874
Pockets: 3 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pomb	protein	149	37% helix, 19% strand	O06874

Ligands and binding sites

ACT · Acetate ion · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	58	0.35	0.78	14	empty
2	61	0.31	0.75	16	empty
3	58	0.31	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 1040 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

3WPW · Structure of PomBc5, a periplasmic fragment of PomB from Vibrio · 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 O06874
Elsewhere: RCSB PDB 3WPW · PDBe 3WPW · UniProt O06874

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