Research workbench
Viral chemokine binding protein M3 from murine GAMMAHERPESVIRUS68 in complex with the cc-chemokine CCL2/MCP-1
Analyse Viral chemokine binding protein M3 from murine GAMMAHERPESVIRUS68 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NZ1
- Type
- protein
- Length
- 1,305 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein GAMMAHV.M3; Small inducible cytokine A2
- UniProt
- O41925, P13500
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, X | Hypothetical protein GAMMAHV.M3 | protein | 371 | 15% helix, 39% strand | O41925 |
| D, E, Y | Small inducible cytokine A2 | protein | 64 | 19% helix, 27% strand | P13500 |
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.77 | 0.80 | 70 | empty |
| 2 | 1144 | 0.77 | 0.79 | 94 | empty |
| 3 | 542 | 0.71 | 0.80 | 37 | empty |
| 4 | 408 | 0.70 | 0.82 | 55 | empty |
| 5 | 54 | 0.61 | 0.92 | 18 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1434 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 613 Ų buried · 8 hydrogen bonds · protein-protein
- B–X · 590 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 582 Ų buried · 8 hydrogen bonds · protein-protein
- X–Y · 555 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 2NZ1 · Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The… · the same entry in another collection · chain Y against Y, TM-score 1.00
- P13500 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 2 (P13500) · a predicted model of the same protein · chain Y against A, TM-score 0.92
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 O41925
- Every structure of UniProt P13500
- Elsewhere: RCSB PDB 2NZ1 · PDBe 2NZ1 · UniProt O41925 · UniProt P13500
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