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Cryoem reconstruction of the HIV GP140 in complex with the extracellular domains of CD4 and the adnectin domain of combinectin. the GP140 and CD4 coordinates from entry 6EDU were rigid body fitted to the EM MAP along withe the crystal structure of CD4+ADNECTIN

Analyse Cryoem reconstruction of the HIV GP140 in complex with the extracellular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7T0O
Type: protein
Length: 2,628 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BG505 SOSIP.664 GP140; T-cell surface glycoprotein CD4; Adnectin
UniProt: P01730
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 10 distinct chains · 11% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	BG505 SOSIP.664 GP140	protein	360	14% helix, 26% strand	—
G	BG505 SOSIP.664 GP140	protein	353	13% helix, 26% strand	—
I	BG505 SOSIP.664 GP140	protein	356	13% helix, 26% strand	—
B	BG505 SOSIP.664 GP140	protein	35	94% helix, 0% strand	—
F, J	BG505 SOSIP.664 GP140	protein	37	89% helix, 0% strand	—
H	T-cell surface glycoprotein CD4	protein	356	2% helix, 51% strand	P01730
O, P, Q	Adnectin	protein	95	0% helix, 54% strand	—
L	T-cell surface glycoprotein CD4	protein	357	3% helix, 47% strand	P01730
M	T-cell surface glycoprotein CD4	protein	353	3% helix, 47% strand	P01730
K, N, R	BG505 SOSIP.664 GP140	protein	33	91% helix, 0% strand	—

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	947	0.82	0.84	99	empty
2	558	0.79	0.85	79	empty
3	942	0.78	0.81	90	empty
4	126	0.71	0.92	32	empty
5	89	0.70	0.94	23	empty

Interfaces

15 interfaces between chains.

H–O · 1022 Å² buried · 12 hydrogen bonds · protein-protein
L–P · 956 Å² buried · 11 hydrogen bonds · protein-protein
M–Q · 955 Å² buried · 11 hydrogen bonds · protein-protein
I–M · 807 Å² buried · 3 hydrogen bonds · protein-protein
D–L · 479 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 33 disulfide (disulfide).

Compared structures

7T0O · cryoEM reconstruction of the HIV gp140 in complex with the extracellular domains of CD4… · the same entry in another collection · chain R against R, 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 P01730
Elsewhere: RCSB PDB 7T0O · PDBe 7T0O · UniProt P01730

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