MolNFT v1 · #187887 · protein
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
7T0O · BG505 SOSIP.664 GP140: “Cryoem reconstruction of the HIV GP140 in complex with the extracellular domains of CD4 and the adnectin…”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #187887 on GenesisL1: 3D…
- 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.
| Volume (ų) | 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 Ų buried · 12 hydrogen bonds · protein-protein
- L–P · 956 Ų buried · 11 hydrogen bonds · protein-protein
- M–Q · 955 Ų buried · 11 hydrogen bonds · protein-protein
- I–M · 807 Ų buried · 3 hydrogen bonds · protein-protein
- D–L · 479 Ų 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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