MolNFT v1 · #120181 · protein
Crystal structure of diabody complex with repebody and mbp
5GS2 · Maltose-binding periplasmic protein: “Crystal structure of diabody complex with repebody and mbp”. X-ray diffraction, 12 pockets (best druggability 0.71). MolNFT v1 #120181 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5GS2
- Type
- protein
- Length
- 1,092 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein; Anti-repebody; Anti-mbp; Repebody
- UniProt
- P0AEX9
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic protein | protein | 367 | 40% helix, 20% strand | P0AEX9 |
| D | Anti-repebody | protein | 226 | 1% helix, 46% strand | — |
| H | Anti-mbp | protein | 231 | 4% helix, 47% strand | — |
| B | Repebody | protein | 268 | 17% helix, 15% strand | — |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.71 | 0.83 | 32 | empty |
| 2 | 244 | 0.62 | 0.81 | 30 | empty |
| 3 | 305 | 0.58 | 0.77 | 42 | empty |
| 4 | 240 | 0.53 | 0.76 | 39 | empty |
| 5 | 68 | 0.48 | 0.84 | 21 | empty |
Interfaces
5 interfaces between chains.
- D–H · 2240 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 927 Ų buried · 8 hydrogen bonds · protein-protein
- D–B · 836 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 464 Ų buried · 8 hydrogen bonds · protein-protein
- H–B · 190 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5GS2 · Crystal structure of diabody complex with repebody and MBP · 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
- Every structure of UniProt P0AEX9
- Elsewhere: RCSB PDB 5GS2 · PDBe 5GS2 · UniProt P0AEX9
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