MolNFT v1 · #157929 · protein

Trypanosoma brucei - BDF5, TB427TMP.01.5000 a, solved with pf-CBP1

6NEZ · Uncharacterized protein: “Trypanosoma brucei - BDF5, TB427TMP.01.5000 a, solved with pf-CBP1”. X-ray diffraction, 2 ligands (KJS, UNX), 7 pockets (best druggability 0.77). MolNFT v1 #157929 on GenesisL1: 3D structure, binding sites…

PDB: 6NEZ
Type: protein
Length: 463 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein
UniProt: Q382J7
Ligands: KJS, UNX
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Uncharacterized protein	protein	116	67% helix, 0% strand	Q382J7
B	Uncharacterized protein	protein	116	67% helix, 0% strand	Q382J7
D	Uncharacterized protein	protein	115	67% helix, 0% strand	Q382J7

Ligands and binding sites

KJS · 5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[2-(morpholin-4-yl) ethyl]-2-[2-(4-propoxyphenyl)ethyl]-1H-benzimidazole · ligand · 4 copies · chains A, B, C, D
UNX · Unknown atom or ion · ion · 5 copies · chains A, D, B, C

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

Pockets

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1037	0.77	0.80	82	UNX
2	99	0.58	0.86	20	KJS
3	106	0.56	0.84	20	KJS
4	219	0.53	0.77	20	empty
5	95	0.53	0.84	18	KJS

Interfaces

5 interfaces between chains.

B–C · 730 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 722 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 427 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 383 Å² buried · 1 hydrogen bond · protein-protein
A–B · 253 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6NEZ · Trypanosoma brucei - BDF5, Tb427tmp.01.5000 A, solved with PF-CBP1 · 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 Q382J7
Elsewhere: RCSB PDB 6NEZ · PDBe 6NEZ · UniProt Q382J7

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