MolNFT v1 · #163617 · protein
Structure of zebov gp in complex with 1T0227 antibody
6S8D · Light chain: “Structure of zebov gp in complex with 1T0227 antibody”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.81). MolNFT v1 #163617 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6S8D
- Type
- protein
- Length
- 1,584 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain; Heavy chain; Envelope glycoprotein
- UniProt
- A0A0U3BWW0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, O, U | Light chain | protein | 110 | 7% helix, 48% strand | — |
| H, P, Y | Heavy chain | protein | 122 | 0% helix, 48% strand | — |
| A, C, E | Envelope glycoprotein | protein | 186 | 6% helix, 42% strand | A0A0U3BWW0 |
| B, D, F | Envelope glycoprotein | protein | 110 | 38% helix, 13% strand | A0A0U3BWW0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, D, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.81 | 0.82 | 111 | empty |
| 2 | 480 | 0.80 | 0.87 | 52 | empty |
| 3 | 547 | 0.79 | 0.85 | 57 | empty |
| 4 | 552 | 0.79 | 0.85 | 59 | empty |
| 5 | 92 | 0.73 | 0.96 | 24 | empty |
Interfaces
30 interfaces between chains.
- F–E · 2677 Ų buried · 22 hydrogen bonds · protein-protein
- D–C · 2674 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2673 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1001 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 995 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6S8D · Structure of ZEBOV GP in complex with 1T0227 antibody · the same entry in another collection · chain L against L, 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 A0A0U3BWW0
- Elsewhere: RCSB PDB 6S8D · PDBe 6S8D · UniProt A0A0U3BWW0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.