MolNFT v1 · #138274 · protein
HIV-1 env BG505 SOSIP.664 H72C-H564C trimer in complex with bnabs PGT122 Fab, 35O22 Fab and NIH45-46 scfv
5WDU · Envelope glycoprotein GP160: “HIV-1 env BG505 SOSIP.664 H72C-H564C trimer in complex with bnabs PGT122 Fab, 35O22 Fab and NIH45-46 scfv”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5WDU
- Type
- protein
- Length
- 5,066 residues
- Chains
- 21
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Bnab NIH45-46 scfv; Bnab PGT122 Fab light chain; Bnab PGT122…
- UniProt
- Q2N0S6, Q2N0S8
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, F, Q | Envelope glycoprotein GP160 | protein | 449 | 12% helix, 37% strand | Q2N0S6 |
| D, W | Bnab NIH45-46 scfv | protein | 223 | 5% helix, 55% strand | — |
| O | Bnab NIH45-46 scfv | protein | 222 | 5% helix, 52% strand | — |
| A, J, R | Envelope glycoprotein GP160 | protein | 126 | 52% helix, 6% strand | Q2N0S8 |
| B, K, S | Bnab PGT122 Fab light chain | protein | 210 | 5% helix, 45% strand | — |
| C, L, T | Bnab PGT122 Fab heavy chain | protein | 228 | 5% helix, 50% strand | — |
| H, M, U | Bnab 35O55 Fab heavy chain | protein | 242 | 7% helix, 50% strand | — |
| I | Bnab 35O22 Fab light chain | protein | 207 | 5% helix, 49% strand | — |
| N, V | Bnab 35O22 Fab light chain | protein | 213 | 5% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 87 copies · chains G, A, H, B, C, D, F, J, M, K, L, O, Q, R, U, S, T, W, N
- MAN · alpha-D-mannopyranose · sugar · 57 copies · chains H, I, D, G, B, C, N, M, O, F, W, K, L, U, V, S, T
- BMA · beta-D-mannopyranose · sugar · 24 copies · chains H, I, C, M, L, W, T
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 | 823 | 0.80 | 0.83 | 62 | empty |
| 2 | 1132 | 0.74 | 0.77 | 122 | empty |
| 3 | 1113 | 0.72 | 0.76 | 103 | empty |
| 4 | 253 | 0.71 | 0.86 | 52 | NAG |
| 5 | 233 | 0.70 | 0.86 | 52 | NAG |
Interfaces
38 interfaces between chains.
- Q–R · 2579 Ų buried · 12 hydrogen bonds · protein-protein
- F–J · 2470 Ų buried · 12 hydrogen bonds · protein-protein
- G–A · 2351 Ų buried · 12 hydrogen bonds · protein-protein
- S–T · 2018 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 2003 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 disulfide, 60 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 5WDU · HIV-1 Env BG505 SOSIP.664 H72C-H564C trimer in complex with bNAbs PGT122 Fab, 35O22 Fab… · the same entry in another collection · chain G against G, 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 Q2N0S6
- Every structure of UniProt Q2N0S8
- Elsewhere: RCSB PDB 5WDU · PDBe 5WDU · UniProt Q2N0S6 · UniProt Q2N0S8
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