MolNFT v1 · #98472 · protein
Crystal structure of HIV-1 YU2 envelope GP120 glycoprotein in complex with CD4-mimetic miniprotein, M48U1, and llama single-domain, broadly neutralizing, co-receptor binding site antibody, JM4
4LAJ · HIV-1 YU2 GP120 envelope glycoprotein: “Crystal structure of HIV-1 YU2 envelope GP120 glycoprotein in complex with CD4-mimetic miniprotein, M48U1…”. X-ray diffraction, 4 ligands (MPT, ACA, NAG), 20 pockets (best druggability 0.85).…
- PDB
- 4LAJ
- Type
- protein
- Length
- 1,954 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 YU2 GP120 envelope glycoprotein; CD4-mimetic miniprotein M48U1; Llama single domain…
- Ligands
- MPT, ACA, NAG, NH2
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J | HIV-1 YU2 GP120 envelope glycoprotein | protein | 337 | 17% helix, 39% strand | — |
| F | HIV-1 YU2 GP120 envelope glycoprotein | protein | 334 | 17% helix, 38% strand | — |
| A | HIV-1 YU2 GP120 envelope glycoprotein | protein | 343 | 18% helix, 37% strand | — |
| B | HIV-1 YU2 GP120 envelope glycoprotein | protein | 341 | 18% helix, 39% strand | — |
| K, D, G, C | CD4-mimetic miniprotein M48U1 | protein | 26 | 35% helix, 31% strand | — |
| H | Llama single domain antibody, JM4 | protein | 124 | 10% helix, 48% strand | — |
| M, L | Llama single domain antibody, JM4 | protein | 123 | 7% helix, 49% strand | — |
| I | Llama single domain antibody, JM4 | protein | 125 | 7% helix, 45% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · 4 copies · chains J, K, A, D, F, G, B, C
- ACA · 6-aminohexanoic acid · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 35 copies · chains J, M, H, F, A, B, L, I
- NH2 · Amino group · ion · 4 copies · chains J, K, A, D, G, B, C
- EDO · 1,2-ethanediol · additive · 7 copies · chains J, K, A, D, B, C
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 | 1019 | 0.85 | 0.86 | 125 | NAG, EDO, ACA |
| 2 | 695 | 0.75 | 0.81 | 90 | MPT, NAG |
| 3 | 875 | 0.74 | 0.78 | 84 | NAG |
| 4 | 790 | 0.72 | 0.77 | 71 | NAG |
| 5 | 354 | 0.66 | 0.80 | 55 | MPT, NAG |
Interfaces
22 interfaces between chains.
- A–B · 1021 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 972 Ų buried · 19 hydrogen bonds · protein-protein
- B–I · 960 Ų buried · 19 hydrogen bonds · protein-protein
- J–H · 958 Ų buried · 19 hydrogen bonds · protein-protein
- F–M · 946 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 31 glycan, 8 covalent, 4 d-amino, 4 modified (disulfide, N-glycosylation, covalent ligand, D-amino acid, nonstandard).
Compared structures
- 4LAJ · Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic… · the same entry in another collection · chain J against J, 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 4LAJ · PDBe 4LAJ
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