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Crystal structure of human T-cell leukemia virus protease, a novel target for anti-cancer design

Analyse Crystal structure of human T-cell leukemia virus protease, a novel target for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2B7F
Type: protein
Length: 722 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HTLV protease; (ACE)APQV(STA)VMHP peptide
EC: 3.4.23.-
UniProt: P10274
Ligands: ACE, PO4
Pockets: 14 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	HTLV protease (EC 3.4.23.-)	protein	116	8% helix, 42% strand	P10274
I, K	(ACE)APQV(STA)VMHP peptide	protein	9	0% helix, 44% strand	—
J	(ACE)APQV(STA)VMHP peptide	protein	8	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains I, K
PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	251	0.60	0.79	20	empty
2	223	0.59	0.79	25	empty
3	262	0.55	0.76	21	empty
4	124	0.48	0.79	27	empty
5	73	0.45	0.82	25	empty

Interfaces

12 interfaces between chains.

C–D · 2067 Å² buried · 42 hydrogen bonds · protein-protein
A–B · 2039 Å² buried · 38 hydrogen bonds · protein-protein
E–F · 2001 Å² buried · 35 hydrogen bonds · protein-protein
A–I · 604 Å² buried · 13 hydrogen bonds · protein-protein
E–K · 602 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified, 2 covalent (nonstandard, covalent ligand).

Compared structures

2B7F · Crystal structure of human T-cell leukemia virus protease, a novel target for anti-cancer… · 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 P10274
Elsewhere: RCSB PDB 2B7F · PDBe 2B7F · UniProt P10274

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