MolNFT v1 · #115544 · protein
Artificial HIV fusion inhibitor AP3 fused to the C-terminus of GP41 nhr
5CMZ · Envelope glycoprotein: “Artificial HIV fusion inhibitor AP3 fused to the C-terminus of GP41 nhr”. X-ray diffraction, 4 ligands (ACE, P4G, NH2). MolNFT v1 #115544 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CMZ
- Type
- protein
- Length
- 154 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein; Artificial HIV entry inhibitor AP3
- UniProt
- Q1HMR5
- Ligands
- ACE, P4G, NH2, SO4
Structure
x-ray diffraction · 4 distinct chains · 89% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein | protein | 43 | 95% helix, 0% strand | Q1HMR5 |
| B | Artificial HIV entry inhibitor AP3 | protein | 32 | 84% helix, 0% strand | — |
| C | Envelope glycoprotein | protein | 45 | 91% helix, 0% strand | Q1HMR5 |
| D | Artificial HIV entry inhibitor AP3 | protein | 34 | 82% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, D
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · chains A
- NH2 · Amino group · ion · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · chains A, C
- EDO · 1,2-ethanediol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- C–D · 573 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 571 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 176 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5CMZ · Artificial HIV fusion inhibitor AP3 fused to the C-terminus of gp41 NHR · 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 Q1HMR5
- Elsewhere: RCSB PDB 5CMZ · PDBe 5CMZ · UniProt Q1HMR5
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