MolNFT v1 · #135589 · protein
Crystal structure of DH511.2 Fab in complex with HIV-1 GP41 mper 662- 683 peptide
5U3K · DH511.2 Fab heavy chain: “Crystal structure of DH511.2 Fab in complex with HIV-1 GP41 mper 662- 683 peptide”. X-ray diffraction, 2 ligands (CA, CL), 7 pockets (best druggability 0.67). MolNFT v1 #135589 on GenesisL1: 3D structure…
- PDB
- 5U3K
- Type
- protein
- Length
- 892 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DH511.2 Fab heavy chain; DH511.2 Fab light chain; GP41 mper peptide
- Ligands
- CA, CL
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | DH511.2 Fab heavy chain | protein | 222 | 7% helix, 53% strand | — |
| L | DH511.2 Fab light chain | protein | 214 | 6% helix, 49% strand | — |
| A | DH511.2 Fab heavy chain | protein | 218 | 7% helix, 55% strand | — |
| B | DH511.2 Fab light chain | protein | 199 | 2% helix, 48% strand | — |
| P | GP41 mper peptide | protein | 20 | 60% helix, 0% strand | — |
| C | GP41 mper peptide | protein | 19 | 63% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.67 | 0.76 | 87 | empty |
| 2 | 362 | 0.58 | 0.76 | 59 | empty |
| 3 | 88 | 0.49 | 0.82 | 23 | empty |
| 4 | 226 | 0.48 | 0.74 | 39 | empty |
| 5 | 63 | 0.36 | 0.78 | 18 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1894 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1845 Ų buried · 19 hydrogen bonds · protein-protein
- H–P · 826 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 15 hydrogen bonds · protein-protein
- H–B · 388 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5U3K · Crystal Structure of DH511.2 Fab in Complex with HIV-1 gp41 MPER 662-683 Peptide · 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 5U3K · PDBe 5U3K
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.