MolNFT v1 · #171762 · protein

X-ray structure of the soluble N-terminal domain of T. cruzi pex-14

6ZFW · Peroxin-14: “X-ray structure of the soluble N-terminal domain of T. cruzi pex-14”. X-ray diffraction, 5 pockets (best druggability 0.62). MolNFT v1 #171762 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZFW
Type: protein
Length: 345 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxin-14
UniProt: A0A2V2WKZ5
Pockets: 5 · best druggability 0.62

Structure

x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxin-14	protein	70	73% helix, 0% strand	A0A2V2WKZ5
B, D	Peroxin-14	protein	69	72% helix, 0% strand	A0A2V2WKZ5
C	Peroxin-14	protein	69	72% helix, 0% strand	A0A2V2WKZ5
E	Peroxin-14	protein	68	75% helix, 0% strand	A0A2V2WKZ5

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains A, B, C, E
BME · Beta-mercaptoethanol · additive · 3 copies · chains A, C, B, D
ACT · Acetate ion · additive · chains E

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	223	0.62	0.81	38	empty
2	70	0.56	0.88	19	empty
3	65	0.50	0.85	18	empty
4	64	0.39	0.79	26	empty
5	86	0.38	0.77	19	BME

Interfaces

5 interfaces between chains.

A–E · 477 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 449 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 428 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 423 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 400 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent (additive adduct).

Compared structures

6ZFW · X-ray structure of the soluble N-terminal domain of T. cruzi PEX-14 · 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 A0A2V2WKZ5
Elsewhere: RCSB PDB 6ZFW · PDBe 6ZFW · UniProt A0A2V2WKZ5

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