MolNFT v1 · #105425 · protein
Crystal structure of the anti-HIV-1 antibody 2.2C in complex with HIV- 1 93UG037 GP120
4R4N · HIV-1 GP120: “Crystal structure of the anti-HIV-1 antibody 2.2C in complex with HIV- 1 93UG037 GP120”. X-ray diffraction, 3 ligands (MPT, NAG, NH2), 20 pockets (best druggability 0.80). MolNFT v1 #105425 on GenesisL1: 3D structure…
- PDB
- 4R4N
- Type
- protein
- Length
- 6,347 residues
- Chains
- 32
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 GP120; M48U1 peptide; Antibody 2.2C light chain; Antibody 2.2C heavy chain
- Ligands
- MPT, NAG, NH2
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 GP120 | protein | 333 | 17% helix, 34% strand | — |
| B | HIV-1 GP120 | protein | 342 | 15% helix, 32% strand | — |
| a, b, e, i, m, p, s, v | M48U1 peptide | protein | 26 | 42% helix, 31% strand | — |
| L, D, G, K, O, R, U, X | Antibody 2.2C light chain | protein | 210 | 5% helix, 50% strand | — |
| I | HIV-1 GP120 | protein | 341 | 13% helix, 30% strand | — |
| H, C, F, J, N, Q, T, W | Antibody 2.2C heavy chain | protein | 220 | 6% helix, 50% strand | — |
| E | HIV-1 GP120 | protein | 329 | 15% helix, 32% strand | — |
| M, S | HIV-1 GP120 | protein | 339 | 15% helix, 33% strand | — |
| P, V | HIV-1 GP120 | protein | 338 | 16% helix, 33% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · 8 copies · chains A, a, B, b, E, e, I, i, M, m, P, p, S, s, V, v
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B, O, I, E, M, P, S, V
- NH2 · Amino group · ion · 8 copies · chains A, a, B, b, E, e, I, i, M, m, P, p, S, s, V, v
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.80 | 0.81 | 123 | MPT |
| 2 | 1159 | 0.80 | 0.81 | 154 | MPT |
| 3 | 964 | 0.79 | 0.80 | 118 | empty |
| 4 | 829 | 0.74 | 0.79 | 83 | MPT, NH2 |
| 5 | 897 | 0.74 | 0.78 | 87 | MPT |
Interfaces
64 interfaces between chains.
- D–C · 2035 Ų buried · 13 hydrogen bonds · protein-protein
- G–F · 1997 Ų buried · 11 hydrogen bonds · protein-protein
- R–Q · 1990 Ų buried · 16 hydrogen bonds · protein-protein
- U–T · 1957 Ų buried · 11 hydrogen bonds · protein-protein
- K–J · 1942 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 99 disulfide, 19 glycan, 16 covalent, 16 modified, 8 d-amino (disulfide, N-glycosylation, covalent ligand, nonstandard, D-amino acid).
Compared structures
- 4R4N · Crystal structure of the anti-hiv-1 antibody 2.2c in complex with hiv-1 93ug037 gp120 · the same entry in another collection · chain B against B, 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 4R4N · PDBe 4R4N
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