MolNFT v1 · #164215 · protein
Crystal structure of cat MDM2-S429E ring domain bound to UBCH5B-ub
6SQR · E3 ubiquitin-protein ligase MDM2: “Crystal structure of cat MDM2-S429E ring domain bound to UBCH5B-ub”. X-ray diffraction, 2 ligands (ZN, NO3), 16 pockets (best druggability 0.72). MolNFT v1 #164215 on GenesisL1: 3D structure…
- PDB
- 6SQR
- Type
- protein
- Length
- 1,151 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; Ubiquitin-conjugating enzyme E2 D2; Ubiquitin-40S…
- EC
- 2.3.2.27, 2.3.2.23, 2.3.2.24
- UniProt
- Q7YRZ8, P62837, J3QTR3, P0CG48
- Ligands
- ZN, NO3
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 69 | 19% helix, 25% strand | Q7YRZ8 |
| B, E, H, K | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 146 | 36% helix, 19% strand | P62837 |
| C, F, L | Ubiquitin-40S ribosomal protein S27A | protein | 77 | 23% helix, 36% strand | J3QTR3 |
| D, J | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 64 | 20% helix, 30% strand | Q7YRZ8 |
| G | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 63 | 21% helix, 29% strand | Q7YRZ8 |
| I | Polyubiquitin-C | protein | 76 | 20% helix, 34% strand | P0CG48 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, D, G, J
- NO3 · Nitrate ion · ion · 3 copies · chains D, G, H, I
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, C, D, B, G, I, J, H, L, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.72 | 0.78 | 66 | EDO |
| 2 | 245 | 0.69 | 0.85 | 38 | empty |
| 3 | 266 | 0.65 | 0.82 | 38 | EDO, NO3 |
| 4 | 145 | 0.60 | 0.85 | 29 | EDO |
| 5 | 137 | 0.58 | 0.84 | 29 | EDO |
Interfaces
22 interfaces between chains.
- A–D · 1398 Ų buried · 12 hydrogen bonds · protein-protein
- G–J · 1358 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 972 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 964 Ų buried · 23 hydrogen bonds · protein-protein
- K–L · 960 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide (isopeptide).
Compared structures
- 6SQR · Crystal structure of Cat MDM2-S429E RING domain bound to UbcH5B-Ub · 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 Q7YRZ8
- Every structure of UniProt P62837
- Every structure of UniProt J3QTR3
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 6SQR · PDBe 6SQR · UniProt Q7YRZ8 · UniProt P62837 · UniProt J3QTR3 · UniProt P0CG48
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