MolNFT v1 · #179511 · protein
EBNA1 peptide AA386-405 with Fab MS39P2W174
7K7R · Fab lc MS39P2W174: “EBNA1 peptide AA386-405 with Fab MS39P2W174”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.83). MolNFT v1 #179511 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7K7R
- Type
- protein
- Length
- 891 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab lc MS39P2W174; Fab hc MS39P2W174; EBNA1 peptide AA386-405
- Ligands
- CL
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fab lc MS39P2W174 | protein | 217 | 6% helix, 52% strand | — |
| B | Fab hc MS39P2W174 | protein | 212 | 8% helix, 51% strand | — |
| C | EBNA1 peptide AA386-405 | protein | 14 | 0% helix, 0% strand | — |
| E | Fab hc MS39P2W174 | protein | 219 | 8% helix, 48% strand | — |
| F | EBNA1 peptide AA386-405 | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.83 | 0.85 | 114 | empty |
| 2 | 178 | 0.54 | 0.79 | 23 | empty |
| 3 | 219 | 0.49 | 0.75 | 37 | empty |
| 4 | 104 | 0.34 | 0.73 | 23 | empty |
| 5 | 61 | 0.31 | 0.75 | 17 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1866 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1628 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 640 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 357 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 345 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7K7R · EBNA1 peptide AA386-405 with Fab MS39p2w174 · 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
- Elsewhere: RCSB PDB 7K7R · PDBe 7K7R
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