MolNFT v1 · #135590 · protein
Crystal structure of DH511.2 Fab in complex with HIV-1 GP41 mper 670- 683 peptide
5U3L · DH511.2 Fab heavy chain: “Crystal structure of DH511.2 Fab in complex with HIV-1 GP41 mper 670- 683 peptide”. X-ray diffraction, 6 pockets (best druggability 0.65). MolNFT v1 #135590 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5U3L
- Type
- protein
- Length
- 912 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
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | DH511.2 Fab heavy chain | protein | 223 | 7% helix, 54% strand | — |
| L | DH511.2 Fab light chain | protein | 214 | 7% helix, 50% strand | — |
| A | DH511.2 Fab heavy chain | protein | 224 | 11% helix, 54% strand | — |
| B | DH511.2 Fab light chain | protein | 213 | 6% helix, 50% strand | — |
| P, C | GP41 mper peptide | protein | 19 | 63% helix, 0% strand | — |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.65 | 0.76 | 74 | empty |
| 2 | 357 | 0.56 | 0.75 | 62 | empty |
| 3 | 102 | 0.51 | 0.82 | 23 | empty |
| 4 | 247 | 0.50 | 0.75 | 37 | empty |
| 5 | 82 | 0.30 | 0.73 | 17 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1938 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1890 Ų buried · 19 hydrogen bonds · protein-protein
- H–P · 773 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 749 Ų buried · 15 hydrogen bonds · protein-protein
- H–B · 369 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5U3L · Crystal Structure of DH511.2 Fab in Complex with HIV-1 gp41 MPER 670-683 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 5U3L · PDBe 5U3L
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