Research workbench
Model of GP120, including variable regions, in complex with CD4 and 17B
Analyse Model of GP120, including variable regions, in complex with CD4 and 17B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J70
- Type
- protein
- Length
- 3,450 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal antibody 17B light chain; Monoclonal antibody 17B heavy chain; T-cell surface…
- UniProt
- P01730, P04578
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 5 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M, R | Monoclonal antibody 17B light chain | protein | 212 | 8% helix, 44% strand | — |
| B, N, S | Monoclonal antibody 17B heavy chain | protein | 210 | 5% helix, 50% strand | — |
| C, O, T | T-cell surface glycoprotein CD4 | protein | 181 | 7% helix, 51% strand | P01730 |
| D, P, U | Envelope glycoprotein GP120 | protein | 470 | 15% helix, 36% strand | P04578 |
| E, Q, V | Envelope glycoprotein GP41 | protein | 77 | 92% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.73 | 0.78 | 78 | empty |
| 2 | 991 | 0.73 | 0.76 | 86 | empty |
| 3 | 899 | 0.73 | 0.77 | 85 | empty |
| 4 | 394 | 0.72 | 0.84 | 56 | empty |
| 5 | 398 | 0.72 | 0.83 | 60 | empty |
Interfaces
18 interfaces between chains.
- R–S · 1642 Ų buried · 15 hydrogen bonds · protein-protein
- M–N · 1641 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1633 Ų buried · 15 hydrogen bonds · protein-protein
- T–U · 1248 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1245 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 3J70 · Model of gp120, including variable regions, in complex with CD4 and 17b · the same entry in another collection · chain V against V, 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 P01730
- Every structure of UniProt P04578
- Elsewhere: RCSB PDB 3J70 · PDBe 3J70 · UniProt P01730 · UniProt P04578
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