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Rhesus macaque anti-HIV V3 antibody DH753 with gp120 V3 ZAM18 peptide

Analyse Rhesus macaque anti-HIV V3 antibody DH753 with gp120 V3 ZAM18 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MNS
Type: protein
Length: 894 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.7
Source: Macaca mulatta; SYNTHETIC CONSTRUCT
Molecule: Envelope glylcoprotein; Ab DH753 heavy chain Fab fragment; Ab DH753 light chain
UniProt: A9Q0A0
Ligands: PO4
Pockets: 12 · best druggability 0.58

Structure

x-ray diffraction · resolution 2.7 · 5 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	Envelope glylcoprotein	protein	14	0% helix, 50% strand	A9Q0A0
H	Ab DH753 heavy chain Fab fragment	protein	222	8% helix, 52% strand	—
L, B	Ab DH753 light chain	protein	211	9% helix, 51% strand	—
Q	Envelope glylcoprotein	protein	13	0% helix, 31% strand	A9Q0A0
A	Ab DH753 heavy chain Fab fragment	protein	223	7% helix, 51% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains P, H, Q, A

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

Pockets

12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	448	0.58	0.74	51	empty
2	245	0.53	0.76	37	empty
3	300	0.50	0.73	42	empty
4	186	0.49	0.77	32	empty
5	192	0.47	0.75	29	empty

Interfaces

8 interfaces between chains.

A–B · 1571 Å² buried · 9 hydrogen bonds · protein-protein
H–L · 1548 Å² buried · 14 hydrogen bonds · protein-protein
Q–A · 453 Å² buried · 1 hydrogen bond · protein-protein
P–H · 446 Å² buried · 1 hydrogen bond · protein-protein
Q–B · 408 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6MNS · Rhesus macaque anti-HIV V3 antibody DH753 with GP120 V3 ZAM18 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 A9Q0A0
Elsewhere: RCSB PDB 6MNS · PDBe 6MNS · UniProt A9Q0A0

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