MolNFT v1 · #122160 · protein
Crystal structure of NIH45-46 Fab germline precursor in complex with 426C.TM1DELTAV1-3 GP120
5IGX: “Crystal structure of NIH45-46 Fab germline precursor in complex with 426C.TM1DELTAV1-3 GP120”. X-ray diffraction, 2 ligands (NAG, BMA), 11 pockets (best druggability 0.76). MolNFT v1 #122160 on GenesisL1: 3D structure, binding sites…
- PDB
- 5IGX
- Type
- protein
- Length
- 716 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 426C.TM1DELTAV1-3 GP120; Germline NIH45-46 Fab heavy chain; Germline NIH45-46 light chain
- Ligands
- NAG, BMA
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | 426C.TM1DELTAV1-3 GP120 | protein | 334 | 18% helix, 37% strand | — |
| H | Germline NIH45-46 Fab heavy chain | protein | 192 | 9% helix, 45% strand | — |
| L | Germline NIH45-46 light chain | protein | 190 | 2% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains G, H
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.76 | 0.85 | 66 | empty |
| 2 | 277 | 0.51 | 0.74 | 35 | empty |
| 3 | 87 | 0.51 | 0.83 | 19 | NAG |
| 4 | 134 | 0.49 | 0.79 | 33 | empty |
| 5 | 115 | 0.45 | 0.79 | 33 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1170 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 878 Ų buried · 23 hydrogen bonds · protein-protein
- G–L · 286 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5IGX · Crystal structure of NIH45-46 Fab germline precursor in complex with 426c.TM1deltaV1-3… · the same entry in another collection · chain G against G, 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 5IGX · PDBe 5IGX
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