Research workbench
Crystal structure of NANOCLAMP3:VHH in complex with mtx
Analyse Crystal structure of NANOCLAMP3:VHH in complex with mtx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RGA
- Type
- protein
- Length
- 1,860 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nano clostridial antibody mimetic protein 3 vhh
- Ligands
- MTX, NA
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, G | Nano clostridial antibody mimetic protein 3 vhh | protein | 265 | 4% helix, 52% strand | — |
| E | Nano clostridial antibody mimetic protein 3 vhh | protein | 270 | 5% helix, 50% strand | — |
Ligands and binding sites
- MTX · Methotrexate · ligand · 7 copies · chains A, B, C, D, E, G, F
- NA · Sodium ion · metal · 14 copies · chains A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.77 | 0.84 | 69 | MTX |
| 2 | 538 | 0.76 | 0.83 | 67 | MTX |
| 3 | 1200 | 0.76 | 0.78 | 110 | MTX |
| 4 | 656 | 0.71 | 0.79 | 76 | empty |
| 5 | 233 | 0.61 | 0.81 | 46 | empty |
Interfaces
8 interfaces between chains.
- A–B · 711 Ų buried · 15 hydrogen bonds · protein-protein
- E–G · 692 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 667 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 511 Ų buried · 2 hydrogen bonds · protein-protein
- B–G · 333 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7RGA · Crystal structure of nanoCLAMP3:VHH in complex with MTX · 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 7RGA · PDBe 7RGA
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