MolNFT v1 · #52367 · protein
Structure of human MDM4 N-terminal domain bound to a single domain antibody
2VYR · MDM4 protein: “Structure of human MDM4 N-terminal domain bound to a single domain antibody”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.68). MolNFT v1 #52367 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VYR
- Type
- protein
- Length
- 1,332 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MDM4 protein; Human single domain antibody
- UniProt
- O15151
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | MDM4 protein | protein | 85 | 46% helix, 21% strand | O15151 |
| E, F, I, J, K, L | Human single domain antibody | protein | 124 | 5% helix, 46% strand | — |
| G | Human single domain antibody | protein | 123 | 10% helix, 46% strand | — |
| H | Human single domain antibody | protein | 125 | 7% helix, 46% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, F, H, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.68 | 0.80 | 39 | empty |
| 2 | 292 | 0.62 | 0.80 | 30 | empty |
| 3 | 314 | 0.60 | 0.78 | 33 | empty |
| 4 | 350 | 0.56 | 0.75 | 39 | SO4 |
| 5 | 68 | 0.54 | 0.87 | 19 | empty |
Interfaces
16 interfaces between chains.
- A–E · 844 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 824 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 815 Ų buried · 8 hydrogen bonds · protein-protein
- C–G · 811 Ų buried · 7 hydrogen bonds · protein-protein
- F–I · 689 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2VYR · Structure of human MDM4 N-terminal domain bound to a single domain antibody · the same entry in another collection · chain L against L, 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 O15151
- Elsewhere: RCSB PDB 2VYR · PDBe 2VYR · UniProt O15151
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