Research workbench
Crystal structure of human anti-HIV-1 GP120 reactive antibody 412D
Analyse Crystal structure of human anti-HIV-1 GP120 reactive antibody 412D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RZG
- Type
- protein
- Length
- 867 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 412D light chain; Fab 412D heavy chain
- Ligands
- GLC, FRU
- Pockets
- 10 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab 412D light chain | protein | 224 | 9% helix, 48% strand | — |
| B | Fab 412D heavy chain | protein | 213 | 5% helix, 50% strand | — |
| C | Fab 412D light chain | protein | 214 | 6% helix, 49% strand | — |
| D | Fab 412D heavy chain | protein | 216 | 5% helix, 49% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 7 copies · chains A, B, C, D
- FRU · beta-D-fructofuranose · sugar · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.60 | 0.78 | 49 | empty |
| 2 | 463 | 0.58 | 0.74 | 54 | empty |
| 3 | 395 | 0.56 | 0.74 | 45 | empty |
| 4 | 88 | 0.43 | 0.79 | 22 | empty |
| 5 | 97 | 0.36 | 0.75 | 21 | GLC, FRU |
Interfaces
4 interfaces between chains.
- A–B · 2003 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1685 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 251 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 199 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 modified (disulfide, sulfation).
Compared structures
- 1RZG · Crystal structure of Human anti-HIV-1 GP120 reactive antibody 412d · 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 1RZG · PDBe 1RZG
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