MolNFT v1 · #116417 · protein

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

5DD0 · Anti-HIV antibody DH570 Fab heavy chain: “Crystal structures in an anti-HIV antibody lineage from immunization of rhesus macaques”. X-ray diffraction, 2 ligands (ACE, NH2), 4 pockets (best druggability 0.44). MolNFT v1 #116417 on…

PDB: 5DD0
Type: protein
Length: 443 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-HIV antibody DH570 Fab heavy chain; Anti-HIV antibody DH570 Fab heavy light; Oligo…
Ligands: ACE, NH2
Pockets: 4 · best druggability 0.44

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Anti-HIV antibody DH570 Fab heavy chain	protein	221	4% helix, 52% strand	—
L	Anti-HIV antibody DH570 Fab heavy light	protein	211	6% helix, 51% strand	—
P	Oligo peptide	protein	11	82% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains P
NH2 · Amino group · ion · chains P

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

Pockets

4 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	167	0.44	0.74	32	empty
2	70	0.29	0.73	18	empty
3	61	0.27	0.73	10	empty
4	53	0.26	0.73	15	empty

Interfaces

2 interfaces between chains.

H–L · 1804 Å² buried · 8 hydrogen bonds · protein-protein
H–P · 551 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

5DD0 · 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 5DD0 · PDBe 5DD0

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