MolNFT v1 · #67205 · protein

Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 in complex with GP41 peptide aldkwd

3IDG · 2F5 Fab light chain: “Crystal structure of the HIV-1 cross neutralizing monoclonal antibody 2F5 in complex with GP41 peptide aldkwd”. X-ray diffraction, 3 pockets (best druggability 0.60). MolNFT v1 #67205 on GenesisL1: 3D…

PDB: 3IDG
Type: protein
Length: 447 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2F5 Fab light chain; 2F5 Fab heavy chain; GP41 mper peptide
Pockets: 3 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2F5 Fab light chain	protein	214	6% helix, 51% strand	—
B	2F5 Fab heavy chain	protein	227	8% helix, 51% strand	—
C	GP41 mper peptide	protein	6	0% helix, 17% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	441	0.60	0.75	53	empty
2	127	0.40	0.74	22	empty
3	64	0.30	0.74	19	empty

Interfaces

3 interfaces between chains.

A–B · 1823 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 328 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 256 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3IDG · Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with… · 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 3IDG · PDBe 3IDG

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