Research workbench
Crystal structure of 3BNC60 Fab germline precursor in complex with 426C.TM4DELTAV1-3 GP120
Analyse Crystal structure of 3BNC60 Fab germline precursor in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FEC
- Type
- protein
- Length
- 2,182 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Germline 3BNC60 heavy chain; Germline 3BNC60 light chain; 426C.TM4DELTAV1-3 GP120
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Germline 3BNC60 heavy chain | protein | 215 | 10% helix, 52% strand | — |
| L | Germline 3BNC60 light chain | protein | 202 | 6% helix, 53% strand | — |
| A | Germline 3BNC60 heavy chain | protein | 214 | 8% helix, 52% strand | — |
| B | Germline 3BNC60 light chain | protein | 209 | 6% helix, 51% strand | — |
| C | 426C.TM4DELTAV1-3 GP120 | protein | 338 | 17% helix, 37% strand | — |
| D | 426C.TM4DELTAV1-3 GP120 | protein | 337 | 17% helix, 36% strand | — |
| G | 426C.TM4DELTAV1-3 GP120 | protein | 338 | 17% helix, 39% strand | — |
| I | 426C.TM4DELTAV1-3 GP120 | protein | 329 | 18% helix, 35% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains C, D, G, I
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains C, D, G, H
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.85 | 0.87 | 131 | empty |
| 2 | 546 | 0.74 | 0.82 | 68 | empty |
| 3 | 940 | 0.73 | 0.77 | 89 | empty |
| 4 | 789 | 0.66 | 0.74 | 82 | empty |
| 5 | 83 | 0.65 | 0.91 | 21 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1653 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1640 Ų buried · 14 hydrogen bonds · protein-protein
- G–I · 765 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 762 Ų buried · 18 hydrogen bonds · protein-protein
- H–I · 760 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide, 19 glycan (disulfide, N-glycosylation).
Compared structures
- 5FEC · Crystal structure of 3BNC60 Fab germline precursor in complex with 426c.TM4deltaV1-3 gp120 · 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 5FEC · PDBe 5FEC
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