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Crystal structure of HIV-1 GP120 core in complex with nbd-11021, a small molecule CD4-antagonist
Analyse Crystal structure of HIV-1 GP120 core in complex with nbd-11021, a small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RZ8
- Type
- protein
- Length
- 1,351 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120
- UniProt
- Q0ED31
- Ligands
- 3ZM, NAG
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Envelope glycoprotein GP120 | protein | 339 | 16% helix, 37% strand | Q0ED31 |
| B | Envelope glycoprotein GP120 | protein | 334 | 17% helix, 38% strand | Q0ED31 |
Ligands and binding sites
- 3ZM · 5-(4-chlorophenyl)-N-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2R)-piperidin-2-yl]methyl}-1H-pyrrole-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.75 | 0.79 | 86 | NAG, EPE |
| 2 | 238 | 0.71 | 0.87 | 45 | NAG |
| 3 | 603 | 0.67 | 0.77 | 68 | NAG |
| 4 | 104 | 0.61 | 0.87 | 27 | 3ZM |
| 5 | 89 | 0.60 | 0.88 | 22 | 3ZM |
Interfaces
3 interfaces between chains.
- B–C · 475 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 440 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 94 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 glycan, 28 disulfide (N-glycosylation, disulfide).
Compared structures
- 4RZ8 · Crystal structure of HIV-1 gp120 core in complex with NBD-11021, a small molecule… · 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 Q0ED31
- Elsewhere: RCSB PDB 4RZ8 · PDBe 4RZ8 · UniProt Q0ED31
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