MolNFT v1 · #122209 · protein
Structure of the unliganded anti-HIV antibody DH501 that binds GP120 V3 glycan and the base of V3
5IIE · Antibody DH501 fabh chain: “Structure of the unliganded anti-HIV antibody DH501 that binds GP120 V3 glycan and the base of V3”. X-ray diffraction, 9 pockets (best druggability 0.70). MolNFT v1 #122209 on GenesisL1: 3D structure…
- PDB
- 5IIE
- Type
- protein
- Length
- 814 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody DH501 fabh chain; Antibody DH501 light chain
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody DH501 fabh chain | protein | 219 | 7% helix, 52% strand | — |
| L | Antibody DH501 light chain | protein | 211 | 9% helix, 51% strand | — |
| A | Antibody DH501 fabh chain | protein | 210 | 9% helix, 50% strand | — |
| B | Antibody DH501 light chain | protein | 174 | 5% helix, 45% strand | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.70 | 0.78 | 55 | empty |
| 2 | 312 | 0.51 | 0.73 | 39 | empty |
| 3 | 158 | 0.41 | 0.74 | 23 | empty |
| 4 | 78 | 0.41 | 0.79 | 27 | empty |
| 5 | 79 | 0.36 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1814 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1777 Ų buried · 10 hydrogen bonds · protein-protein
- H–A · 971 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5IIE · Structure of the unliganded anti-HIV antibody DH501 that binds GP120 V3 glycan and the… · the same entry in another collection · chain H against H, 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 5IIE · PDBe 5IIE
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