Research workbench
Crystal structure of DH650 Fab from a rhesus macaque in complex with HIV-1 GP120 core
Analyse Crystal structure of DH650 Fab from a rhesus macaque in complex with HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XCJ
- Type
- protein
- Length
- 721 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; DH650 Fab heavy chain; DH650 Fab light chain
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP120 | protein | 279 | 16% helix, 38% strand | — |
| H | DH650 Fab heavy chain | protein | 223 | 8% helix, 50% strand | — |
| L | DH650 Fab light chain | protein | 219 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains G, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.69 | 0.97 | 21 | empty |
| 2 | 261 | 0.58 | 0.78 | 44 | empty |
| 3 | 56 | 0.57 | 0.90 | 21 | empty |
| 4 | 333 | 0.53 | 0.74 | 44 | empty |
| 5 | 256 | 0.52 | 0.75 | 33 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1799 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 727 Ų buried · 13 hydrogen bonds · protein-protein
- G–L · 569 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6XCJ · Crystal Structure of DH650 Fab from a Rhesus Macaque in Complex with HIV-1 gp120 Core · the same entry in another collection · chain G against G, 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 6XCJ · PDBe 6XCJ
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