MolNFT v1 · #145940 · protein
Crystal structure of ioma-class CLK31 Fab from an HIV-1 naive donor in complex with a germline-targeting GP120 engineered outer domain eod- GT8 at 2.6 a
6D2P · Germline-targeting HIV-1 GP120 engineered outer domain eod…: “Crystal structure of ioma-class CLK31 Fab from an HIV-1 naive donor in complex with a germline-targeting…”. X-ray diffraction, 5 pockets (best druggability 0.68). MolNFT…
- PDB
- 6D2P
- Type
- protein
- Length
- 592 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Germline-targeting HIV-1 GP120 engineered outer domain eod- GT8; Iomaclass naive CLK31…
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Germline-targeting HIV-1 GP120 engineered outer domain eod- GT8 | protein | 169 | 18% helix, 37% strand | — |
| H | Iomaclass naive CLK31 Fab heavy chain | protein | 213 | 8% helix, 49% strand | — |
| L | Iomaclass naive CLK31 Fab light chain | protein | 210 | 6% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.68 | 0.80 | 62 | empty |
| 2 | 325 | 0.52 | 0.73 | 43 | empty |
| 3 | 147 | 0.50 | 0.79 | 27 | GOL |
| 4 | 168 | 0.47 | 0.76 | 28 | empty |
| 5 | 50 | 0.32 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1632 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 846 Ų buried · 22 hydrogen bonds · protein-protein
- C–L · 264 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6D2P · Crystal structure of IOMA-class CLK31 Fab from an HIV-1 naive donor in complex with a… · the same entry in another collection · chain C against C, 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 6D2P · PDBe 6D2P
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