MolNFT v1 · #175715 · protein
Crystal structure of kaposi sarcoma associated herpesvirus (kshv ) ghgl in complex with the ligand binding domian (lbd) of EPHA2
7CZF · Ephrin type-a receptor 2: “Crystal structure of kaposi sarcoma associated herpesvirus (kshv ) ghgl in complex with the ligand binding…”. X-ray diffraction, 3 ligands (NAG, FUC, MAN), 20 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 7CZF
- Type
- protein
- Length
- 1,843 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ephrin type-a receptor 2; Envelope glycoprotein H; Envelope glycoprotein L
- EC
- 2.7.10.1
- UniProt
- P29317, Q98142, Q76RG7
- Ligands
- NAG, FUC, MAN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 170 | 0% helix, 47% strand | P29317 |
| B | Envelope glycoprotein H | protein | 644 | 37% helix, 18% strand | Q98142 |
| C | Envelope glycoprotein L | protein | 114 | 40% helix, 12% strand | Q76RG7 |
| D | Ephrin type-a receptor 2 (EC 2.7.10.1) | protein | 158 | 0% helix, 49% strand | P29317 |
| E | Envelope glycoprotein H | protein | 642 | 36% helix, 18% strand | Q98142 |
| F | Envelope glycoprotein L | protein | 115 | 36% helix, 15% strand | Q76RG7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains E, F, B, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains F, D, E, A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.75 | 0.98 | 18 | empty |
| 2 | 65 | 0.74 | 0.98 | 17 | empty |
| 3 | 647 | 0.70 | 0.78 | 73 | empty |
| 4 | 141 | 0.61 | 0.85 | 24 | empty |
| 5 | 232 | 0.57 | 0.78 | 25 | empty |
Interfaces
9 interfaces between chains.
- E–F · 2641 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 2573 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1149 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1112 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 600 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 7CZF · Crystal structure of Kaposi Sarcoma associated herpesvirus (KSHV ) gHgL in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- P29317 · AlphaFold monomer V2.0 prediction for ephrin type-a receptor 2 (P29317) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P29317
- Every structure of UniProt Q98142
- Every structure of UniProt Q76RG7
- Elsewhere: RCSB PDB 7CZF · PDBe 7CZF · UniProt P29317 · UniProt Q98142 · UniProt Q76RG7
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