Research workbench
Crystal structure of MINDY2 (C266A) in complex with LYS48-linked penta-ubiquitin (K48-UB5)
Analyse Crystal structure of MINDY2 (C266A) in complex with LYS48-linked… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NPI
- Type
- protein
- Length
- 4,455 residues
- Chains
- 42
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase mindy-2; Polyubiquitin-C
- EC
- 3.4.19.12
- UniProt
- Q8NBR6, P0CG48
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Ubiquitin carboxyl-terminal hydrolase mindy-2 (EC 3.4.19.12) | protein | 262 | 38% helix, 21% strand | Q8NBR6 |
| B, H, N, T, Z, c, f, i, l | Polyubiquitin-C | protein | 73 | 25% helix, 36% strand | P0CG48 |
| C, D, F, I, J, L, O, P, R, U, V, X, a, b, d, g, h, j, m, p | Polyubiquitin-C | protein | 76 | 20% helix, 34% strand | P0CG48 |
| E, n | Polyubiquitin-C | protein | 75 | 19% helix, 33% strand | P0CG48 |
| K | Polyubiquitin-C | protein | 74 | 23% helix, 35% strand | P0CG48 |
| M, S, Y, e, k | Ubiquitin carboxyl-terminal hydrolase mindy-2 (EC 3.4.19.12) | protein | 263 | 38% helix, 19% strand | Q8NBR6 |
| Q | Polyubiquitin-C | protein | 71 | 24% helix, 31% strand | P0CG48 |
| W, o | Polyubiquitin-C | protein | 72 | 21% helix, 31% strand | P0CG48 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.79 | 0.81 | 72 | empty |
| 2 | 908 | 0.78 | 0.81 | 71 | empty |
| 3 | 974 | 0.77 | 0.79 | 89 | empty |
| 4 | 798 | 0.76 | 0.80 | 96 | empty |
| 5 | 681 | 0.75 | 0.81 | 55 | empty |
Interfaces
79 interfaces between chains.
- A–E · 1176 Ų buried · 19 hydrogen bonds · protein-protein
- e–i · 1159 Ų buried · 18 hydrogen bonds · protein-protein
- M–Q · 1138 Ų buried · 19 hydrogen bonds · protein-protein
- S–W · 1102 Ų buried · 17 hydrogen bonds · protein-protein
- k–o · 1081 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 isopeptide (isopeptide).
Compared structures
- 7NPI · Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) · the same entry in another collection · chain K against K, 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 Q8NBR6
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 7NPI · PDBe 7NPI · UniProt Q8NBR6 · UniProt P0CG48
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