Research workbench
Crystal structure of the clade B isolate B41 mutant fusion peptide (residues 512-521) in complex with VRC34.01
Analyse Crystal structure of the clade B isolate B41 mutant fusion peptide (residues… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ME1
- Type
- protein
- Length
- 896 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VRC34.01 Fab heavy chain; VRC34.01 Fab light chain; Envelope glycoprotein GP160
- UniProt
- P03375
- Pockets
- 11 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | VRC34.01 Fab heavy chain | protein | 223 | 11% helix, 49% strand | — |
| B, D | VRC34.01 Fab light chain | protein | 212 | 7% helix, 50% strand | — |
| F | Envelope glycoprotein GP160 | protein | 10 | 0% helix, 0% strand | P03375 |
| E | Envelope glycoprotein GP160 | protein | 16 | 0% helix, 0% strand | P03375 |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.58 | 0.75 | 46 | empty |
| 2 | 303 | 0.57 | 0.77 | 36 | empty |
| 3 | 212 | 0.52 | 0.77 | 34 | empty |
| 4 | 284 | 0.51 | 0.74 | 35 | empty |
| 5 | 202 | 0.51 | 0.76 | 35 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1854 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1814 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 713 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 504 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 438 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6ME1 · Crystal structure of the clade B isolate B41 mutant fusion peptide (residues 512-521) in… · 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
- Every structure of UniProt P03375
- Elsewhere: RCSB PDB 6ME1 · PDBe 6ME1 · UniProt P03375
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