MolNFT v1 · #69224 · protein

Uncharacterized protein BP1543 from bordetella pertussis tohama I

3KK4: “Uncharacterized protein BP1543 from bordetella pertussis tohama I”. X-ray diffraction, 6 pockets (best druggability 0.67). MolNFT v1 #69224 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3KK4
Type: protein
Length: 500 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein BP1543
UniProt: Q7VY20
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Uncharacterized protein BP1543	protein	125	54% helix, 13% strand	Q7VY20

Ligands and binding sites

ACT · Acetate ion · additive · chains A, B
GOL · Glycerol · additive · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	536	0.67	0.78	41	GOL
2	69	0.37	0.78	16	ACT
3	68	0.35	0.77	18	empty
4	56	0.31	0.76	13	empty
5	60	0.28	0.74	19	empty

Interfaces

4 interfaces between chains.

A–B · 3144 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 3141 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 335 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 189 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered, artifact).

Compared structures

3KK4 · uncharacterized protein BP1543 from Bordetella pertussis Tohama I · 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 Q7VY20
Elsewhere: RCSB PDB 3KK4 · PDBe 3KK4 · UniProt Q7VY20

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