MolNFT v1 · #127188 · protein
XCPQN012 in complex with VHH04
5MP2 · Type II secretion system protein D: “XCPQN012 in complex with VHH04”. X-ray diffraction, 7 pockets (best druggability 0.53). MolNFT v1 #127188 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MP2
- Type
- protein
- Length
- 674 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II secretion system protein D; Camelid nanobody VHH04
- UniProt
- A0A0A8RG33
- Pockets
- 7 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II secretion system protein D | protein | 214 | 39% helix, 28% strand | A0A0A8RG33 |
| B | Type II secretion system protein D | protein | 212 | 36% helix, 28% strand | A0A0A8RG33 |
| C | Camelid nanobody VHH04 | protein | 123 | 5% helix, 52% strand | — |
| D | Camelid nanobody VHH04 | protein | 125 | 10% helix, 50% strand | — |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.53 | 0.75 | 37 | empty |
| 2 | 129 | 0.43 | 0.76 | 16 | empty |
| 3 | 144 | 0.42 | 0.75 | 25 | empty |
| 4 | 145 | 0.40 | 0.73 | 29 | empty |
| 5 | 76 | 0.38 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 943 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 589 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 585 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5MP2 · XcpQN012 in complex with VHH04 · 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 A0A0A8RG33
- Elsewhere: RCSB PDB 5MP2 · PDBe 5MP2 · UniProt A0A0A8RG33
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