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Crystal structures in an anti-HIV antibody lineage from immunization of rhesus macaques

Analyse Crystal structures in an anti-HIV antibody lineage from immunization of rhesus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DD3
Type: protein
Length: 435 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-HIV antibody DH570.4 Fab heavy chain; Anti-HIV antibody DH570.4 Fab light chain
Pockets: 6 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Anti-HIV antibody DH570.4 Fab heavy chain	protein	222	8% helix, 51% strand	—
L	Anti-HIV antibody DH570.4 Fab light chain	protein	213	7% helix, 51% strand	—

Pockets

6 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	318	0.52	0.74	46	empty
2	71	0.50	0.85	20	empty
3	203	0.48	0.75	35	empty
4	67	0.32	0.75	15	empty
5	67	0.28	0.73	15	empty

Interfaces

1 interface between chains.

H–L · 1847 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5DD3 · Crystal structures in an anti-HIV antibody lineage from immunization of Rhesus macaques · the same entry in another collection · chain H against H, 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 5DD3 · PDBe 5DD3

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