MolNFT v1 · #11517 · protein

Crystal structure of the single-chain fv fragment 1696 in complex with the epitope peptide corresponding to N- terminus of HIV-1 protease

1JP5: “Crystal structure of the single-chain fv fragment 1696 in complex with the epitope peptide corresponding to…”. X-ray diffraction, 3 pockets (best druggability 0.32). MolNFT v1 #11517 on GenesisL1: 3D structure, binding sites and…

PDB: 1JP5
Type: protein
Length: 476 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-chain fv fragment 1696; Epitope peptide corresponding to N-terminus of HIV-1…
Pockets: 3 · best druggability 0.32

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Single-chain fv fragment 1696	protein	232	5% helix, 51% strand	—
C, D	Epitope peptide corresponding to N-terminus of HIV-1 protease	protein	6	0% helix, 0% strand	—

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	71	0.32	0.75	15	empty
2	50	0.28	0.75	14	empty
3	66	0.28	0.72	21	empty

Interfaces

2 interfaces between chains.

A–C · 560 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 550 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1JP5 · Crystal structure of the single-chain Fv fragment 1696 in complex with the epitope… · 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
Elsewhere: RCSB PDB 1JP5 · PDBe 1JP5

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