MolNFT v1 · #156639 · protein
HIV-1 envelope glycoprotein clone BG505 delct N332T in complex with broadly neutralizing antibody Fab PGT151
6MAR · Immunoglobulin G PGT151 Fab, heavy chain: “HIV-1 envelope glycoprotein clone BG505 delct N332T in complex with broadly neutralizing antibody Fab PGT151”. Electron microscopy, 5 ligands (NAG, MAN, BMA), 20 pockets (best druggability…
- PDB
- 6MAR
- Type
- protein
- Length
- 2,225 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin G PGT151 Fab, heavy chain; Immunoglobulin G PGT151, light chain; Envelope…
- UniProt
- Q2N0S6, Q2N0S7
- Ligands
- NAG, MAN, BMA, GAL, FUC
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 10 distinct chains · 17% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Immunoglobulin G PGT151 Fab, heavy chain | protein | 135 | 4% helix, 39% strand | — |
| N | Immunoglobulin G PGT151, light chain | protein | 112 | 3% helix, 39% strand | — |
| H | Immunoglobulin G PGT151 Fab, heavy chain | protein | 135 | 2% helix, 41% strand | — |
| L | Immunoglobulin G PGT151, light chain | protein | 114 | 0% helix, 33% strand | — |
| A | Envelope glycoprotein GP160 | protein | 440 | 13% helix, 33% strand | Q2N0S6 |
| B | Envelope glycoprotein GP160 | protein | 134 | 49% helix, 2% strand | Q2N0S7 |
| D | Envelope glycoprotein GP160 | protein | 146 | 47% helix, 5% strand | Q2N0S7 |
| C | Envelope glycoprotein GP160 | protein | 444 | 10% helix, 32% strand | Q2N0S6 |
| E | Envelope glycoprotein GP160 | protein | 438 | 14% helix, 32% strand | Q2N0S6 |
| F | Envelope glycoprotein GP160 | protein | 127 | 53% helix, 1% strand | Q2N0S7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 95 copies · chains A, C, B, H, D, L, E, F, M, N
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains A, H, L, E, M, N
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains H, M
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains H, D, L, M, B, N
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains H, B, M, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.86 | 0.87 | 144 | empty |
| 2 | 1191 | 0.85 | 0.85 | 134 | empty |
| 3 | 650 | 0.82 | 0.87 | 97 | NAG |
| 4 | 530 | 0.81 | 0.87 | 84 | empty |
| 5 | 1200 | 0.79 | 0.80 | 113 | empty |
Interfaces
24 interfaces between chains.
- A–B · 2482 Ų buried · 10 hydrogen bonds · protein-protein
- D–C · 2342 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 2341 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1079 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 924 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 glycan, 34 disulfide (N-glycosylation, disulfide).
Compared structures
- 6MAR · HIV-1 Envelope Glycoprotein Clone BG505 delCT N332T in complex with broadly neutralizing… · the same entry in another collection · chain M against M, 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 Q2N0S6
- Every structure of UniProt Q2N0S7
- Elsewhere: RCSB PDB 6MAR · PDBe 6MAR · UniProt Q2N0S6 · UniProt Q2N0S7
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