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Crystal structure of HIV-GP120 core in complex with CD4-binding site antibody B13, space group C2221

Analyse Crystal structure of HIV-GP120 core in complex with CD4-binding site antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IDY
Type: protein
Length: 1,495 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 HXBC2 GP120 core; Fab B13 heavy chain; Fab B13 light chain
Ligands: NAG, SO4
Pockets: 13 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	HIV-1 HXBC2 GP120 core	protein	306	14% helix, 42% strand	—
H, B	Fab B13 heavy chain	protein	229	7% helix, 43% strand	—
L, C	Fab B13 light chain	protein	214	7% helix, 49% strand	—
A	HIV-1 HXBC2 GP120 core	protein	303	14% helix, 42% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains G, H, A, B
SO4 · Sulfate ion · ion · chains G

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

Pockets

13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	720	0.78	0.83	96	empty
2	721	0.77	0.82	102	empty
3	968	0.77	0.79	107	empty
4	724	0.65	0.74	62	empty
5	660	0.64	0.74	66	empty

Interfaces

9 interfaces between chains.

H–L · 2051 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1930 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 768 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 735 Å² buried · 13 hydrogen bonds · protein-protein
H–B · 179 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 glycan, 26 disulfide (N-glycosylation, disulfide).

Compared structures

3IDY · Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space… · the same entry in another collection · chain G against G, 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 3IDY · PDBe 3IDY

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