MolNFT v1 · #157834 · protein
AMC011 V4.2 sosip env trimer in complex with fusion peptide targeting antibody ACS202 fragment antigen binding
6NC2 · AMC011 V4.2 sosip GP120: “AMC011 V4.2 sosip env trimer in complex with fusion peptide targeting antibody ACS202 fragment antigen binding”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.79). MolNFT…
- PDB
- 6NC2
- Type
- protein
- Length
- 4,830 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMC011 V4.2 sosip GP120; AMC011 V4.2 sosip GP41; Monoclonal antibody ACS202 fragment…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G | AMC011 V4.2 sosip GP120 | protein | 436 | 15% helix, 38% strand | — |
| B, I, J, K, M, N | AMC011 V4.2 sosip GP41 | protein | 129 | 65% helix, 9% strand | — |
| H, O, P, Q, R, S | Monoclonal antibody ACS202 fragment antigen binding heavy chain | protein | 132 | 2% helix, 55% strand | — |
| L, T, U, V, W, X | Monoclonal antibody ACS202 fragment antigen binding kappa chain | protein | 108 | 3% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 78 copies · chains A, B, H, C, I, O, D, J, P, E, K, Q, F, M, R, G, N, S
- MAN · alpha-D-mannopyranose · sugar · 42 copies · chains H, A, O, C, P, D, Q, E, R, F, S, G
- BMA · beta-D-mannopyranose · sugar · 18 copies · chains H, O, P, Q, R, S
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 | 769 | 0.79 | 0.83 | 87 | empty |
| 2 | 866 | 0.79 | 0.82 | 98 | empty |
| 3 | 52 | 0.72 | 0.98 | 20 | empty |
| 4 | 330 | 0.72 | 0.84 | 60 | NAG |
| 5 | 371 | 0.72 | 0.83 | 61 | NAG |
Interfaces
51 interfaces between chains.
- C–I · 2450 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2448 Ų buried · 23 hydrogen bonds · protein-protein
- D–J · 2442 Ų buried · 23 hydrogen bonds · protein-protein
- E–K · 2441 Ų buried · 23 hydrogen bonds · protein-protein
- G–N · 2440 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 disulfide, 54 glycan (disulfide, N-glycosylation).
Compared structures
- 6NC2 · AMC011 v4.2 SOSIP Env trimer in complex with fusion peptide targeting antibody ACS202… · 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 6NC2 · PDBe 6NC2
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