MolNFT v1 · #111629 · protein

Crystal structure of 830A in complex with V1V2

4YWG · Light chain of anti-HIV-1 GP120 V1V2 antibody 830A: “Crystal structure of 830A in complex with V1V2”. X-ray diffraction, 1 ligand (NAG), 18 pockets (best druggability 0.72). MolNFT v1 #111629 on GenesisL1: 3D structure, binding…

PDB: 4YWG
Type: protein
Length: 1,054 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain of anti-HIV-1 GP120 V1V2 antibody 830A; Heavy chain of anti-HIV-1 GP120 V1V2…
Ligands: NAG
Pockets: 18 · best druggability 0.72

Structure

x-ray diffraction · 6 distinct chains · 6% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Light chain of anti-HIV-1 GP120 V1V2 antibody 830A	protein	206	6% helix, 41% strand	—
H	Heavy chain of anti-HIV-1 GP120 V1V2 antibody 830A	protein	210	4% helix, 46% strand	—
G	Scaffold HIV-1 GP120 V1V2 region derived from strain ZM109	protein	103	16% helix, 50% strand	—
M	Light chain of anti-HIV-1 GP120 V1V2 antibody 830A	protein	215	6% helix, 48% strand	—
I	Heavy chain of anti-HIV-1 GP120 V1V2 antibody 830A	protein	226	4% helix, 47% strand	—
Q	Scaffold HIV-1 GP120 V1V2 region derived from strain ZM109	protein	94	9% helix, 39% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains G, Q

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

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1092	0.72	0.76	125	empty
2	288	0.67	0.82	45	empty
3	376	0.65	0.79	49	empty
4	382	0.64	0.79	43	empty
5	306	0.62	0.79	47	empty

Interfaces

7 interfaces between chains.

M–I · 1895 Å² buried · 15 hydrogen bonds · protein-protein
L–H · 1655 Å² buried · 13 hydrogen bonds · protein-protein
H–I · 1016 Å² buried · 12 hydrogen bonds · protein-protein
H–G · 409 Å² buried · 5 hydrogen bonds · protein-protein
I–Q · 401 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

4YWG · Crystal structure of 830A in complex with V1V2 · the same entry in another collection · chain L against L, 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 4YWG · PDBe 4YWG

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