MolNFT v1 · #167607 · protein
Nanodisc of full-length HIV-1 envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three 10E8 fabs
6VPX: “Nanodisc of full-length HIV-1 envelope glycoprotein clone AMC011 in complex with one PGT151 Fab and three…”. Electron microscopy, 6 ligands (44E, NAG, MAN). MolNFT v1 #167607 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6VPX
- Type
- protein
- Length
- 2,684 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Ligands
- 44E, NAG, MAN, BMA, FUC, GAL
Structure
electron microscopy · 11 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 430 | — | — |
| E | — | protein | 419 | — | — |
| C | — | protein | 438 | — | — |
| D | — | protein | 129 | — | — |
| B | — | protein | 143 | — | — |
| F | — | protein | 120 | — | — |
| H, K, M | — | protein | 129 | — | — |
| L, N, O | — | protein | 108 | — | — |
| G, I, J | — | protein | 17 | — | — |
| P | — | protein | 134 | — | — |
| Q | — | protein | 109 | — | — |
Ligands and binding sites
- 44E · (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate · ligand · 3 copies · chains H, L, K, N, M, O
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 90 copies · chains A, E, C, D, B, P, Q, F, M
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains C, P
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains P
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains C, D, Q, B, P
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains Q, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 6VPX · Nanodisc of full-length HIV-1 Envelope glycoprotein clone AMC011 in complex with one… · the same entry in another collection · chain A against A, 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 6VPX · PDBe 6VPX
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