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Crystal structure of glycosylated 426C HIV-1 GP120 core G459C in complex with GLVRC01 A60C heavy chain
Analyse Crystal structure of glycosylated 426C HIV-1 GP120 core G459C 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
- 6MFT
- Type
- protein
- Length
- 1,520 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain GLVRC01; Light chain GLVRC01; GP120
- Ligands
- NAG, MAN, BMA
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain GLVRC01 | protein | 216 | 6% helix, 50% strand | — |
| L | Light chain GLVRC01 | protein | 208 | 6% helix, 50% strand | — |
| A | Heavy chain GLVRC01 | protein | 215 | 4% helix, 51% strand | — |
| B | Light chain GLVRC01 | protein | 209 | 5% helix, 51% strand | — |
| G, C | GP120 | protein | 336 | 16% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains L, G, C, B, H, A
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains G, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- EDO · 1,2-ethanediol · additive · 2 copies · chains C
- PEG · Di(hydroxyethyl)ether · additive · chains H, G
- CIT · Citric acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.76 | 0.82 | 75 | empty |
| 2 | 554 | 0.75 | 0.82 | 63 | PEG |
| 3 | 354 | 0.61 | 0.78 | 31 | NAG |
| 4 | 91 | 0.54 | 0.84 | 19 | NAG |
| 5 | 76 | 0.53 | 0.86 | 18 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1698 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1664 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 846 Ų buried · 19 hydrogen bonds · protein-protein
- H–G · 817 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 325 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 17 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 6MFT · Crystal structure of glycosylated 426c HIV-1 gp120 core G459C in complex with glVRC01… · 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 6MFT · PDBe 6MFT
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