Research workbench
AMC011 V4.2 sosip env trimer in complex with fusion peptide targeting antibody ACS202 fragment antigen binding
Analyse AMC011 V4.2 sosip env trimer in complex with fusion peptide targeting antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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