MolNFT v1 · #147199 · protein
Backbone model based on cryo-EM MAP at 8.5 a of domain-swapped, glycan-reactive, neutralizing antibody 2G12 bound to HIV-1 env BG505 ds-sosip, which was also bound to CD4-binding site antibody VRC03
6E5P · 2G12 light chain: “Backbone model based on cryo-EM MAP at 8.5 a of domain-swapped, glycan-reactive, neutralizing antibody 2G12…”. Electron microscopy, 3 ligands (MAN, NAG, BMA), 20 pockets (best druggability 0.74). MolNFT v1 #147199…
- PDB
- 6E5P
- Type
- protein
- Length
- 5,046 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2G12 light chain; 2G12 heavy chain; Envelope glycoprotein GP120; Envelope glycoprotein…
- UniProt
- Q2N0S6, Q2N0S9
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 6 distinct chains · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 4, K, L, Q, T | 2G12 light chain | protein | 212 | 5% helix, 35% strand | — |
| 2, 3, H, M, R, S | 2G12 heavy chain | protein | 225 | 8% helix, 44% strand | — |
| A, C, E | Envelope glycoprotein GP120 | protein | 453 | 14% helix, 39% strand | Q2N0S6 |
| B, D, F | Envelope glycoprotein GP160 | protein | 126 | 52% helix, 6% strand | Q2N0S9 |
| I, O, V | VRC03 heavy chain | protein | 128 | 7% helix, 50% strand | — |
| J, P, W | VRC03 light chain | protein | 101 | 3% helix, 50% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 54 copies · chains 2, 1, 3, 4, H, M, S, R, L, K, Q, T
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains E, A, C
- BMA · beta-D-mannopyranose · sugar · 12 copies
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 | 947 | 0.74 | 0.79 | 74 | empty |
| 2 | 924 | 0.74 | 0.79 | 77 | empty |
| 3 | 943 | 0.74 | 0.79 | 78 | empty |
| 4 | 917 | 0.74 | 0.79 | 76 | empty |
| 5 | 933 | 0.74 | 0.78 | 76 | empty |
Interfaces
42 interfaces between chains.
- A–B · 621 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 620 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 619 Ų buried · 6 hydrogen bonds · protein-protein
- K–M · 215 Ų buried · 0 hydrogen bonds · protein-protein
- Q–R · 215 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6E5P · Backbone model based on cryo-EM map at 8.5 A of domain-swapped, glycan-reactive… · the same entry in another collection · chain 1 against 1, 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 Q2N0S9
- Elsewhere: RCSB PDB 6E5P · PDBe 6E5P · UniProt Q2N0S6 · UniProt Q2N0S9
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