MolNFT v1 · #46208 · protein

Structure of HIV-1 protease D25N complexed with the rt-rh analogue peptide gly-ala-glu-val-PHE*TYR-val-asp-gly-ala

2NXL · Protease retropepsin: “Structure of HIV-1 protease D25N complexed with the rt-rh analogue peptide…”. X-ray diffraction, 1 ligand (PO4). MolNFT v1 #46208 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2NXL
Type: protein
Length: 207 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease retropepsin; Analogue of rt-rh pol protease substrate peptide
EC: 3.4.23.16
UniProt: O38732
Ligands: PO4

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protease retropepsin (EC 3.4.23.16)	protein	99	4% helix, 56% strand	O38732
P	Analogue of rt-rh pol protease substrate peptide	protein	9	0% helix, 44% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains B, A

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

Interfaces

3 interfaces between chains.

A–B · 1831 Å² buried · 41 hydrogen bonds · protein-protein
B–P · 548 Å² buried · 9 hydrogen bonds · protein-protein
A–P · 521 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2NXL · Structure of HIV-1 protease D25N complexed with the rt-rh analogue peptide… · 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 O38732
Elsewhere: RCSB PDB 2NXL · PDBe 2NXL · UniProt O38732

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