MolNFT v1 · #157077 · protein

Rhesus macaque anti-HIV V3 antibody DH753 with GP120 V3 ZAM18 peptide

6MNS · Envelope glylcoprotein: “Rhesus macaque anti-HIV V3 antibody DH753 with GP120 V3 ZAM18 peptide”. X-ray diffraction, 1 ligand (PO4), 12 pockets (best druggability 0.58). MolNFT v1 #157077 on GenesisL1: 3D structure, binding sites and…

PDB: 6MNS
Type: protein
Length: 894 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
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 · 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 P against P, 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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