MolNFT v1 · #114758 · protein
Crystal structure of pcdn-27A, an antibody from the pcdn family of HIV-1 antibodies
5BZD · 5G8 HIV antibody light chain: “Crystal structure of pcdn-27A, an antibody from the pcdn family of HIV-1 antibodies”. X-ray diffraction, 11 pockets (best druggability 0.67). MolNFT v1 #114758 on GenesisL1: 3D structure, binding sites…
- PDB
- 5BZD
- Type
- protein
- Length
- 882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5G8 HIV antibody light chain; 5G8 HIV antibody heavy chain
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5G8 HIV antibody light chain | protein | 213 | 6% helix, 56% strand | — |
| B | 5G8 HIV antibody heavy chain | protein | 229 | 6% helix, 49% strand | — |
| C | 5G8 HIV antibody light chain | protein | 214 | 8% helix, 52% strand | — |
| D | 5G8 HIV antibody heavy chain | protein | 226 | 7% helix, 51% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.67 | 0.74 | 64 | empty |
| 2 | 693 | 0.66 | 0.75 | 57 | empty |
| 3 | 394 | 0.60 | 0.76 | 48 | empty |
| 4 | 258 | 0.54 | 0.76 | 34 | empty |
| 5 | 54 | 0.45 | 0.85 | 21 | GOL |
Interfaces
3 interfaces between chains.
- C–D · 1765 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1646 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 248 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5BZD · Crystal Structure of PCDN-27A, an antibody from the PCDN family of HIV-1 antibodies · 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 5BZD · PDBe 5BZD
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