MolNFT v1 · #113599 · protein
Muts in complex with the N-terminal domain of mutl - crystal form 3
5AKD · DNA mismatch repair protein muts: “Muts in complex with the N-terminal domain of mutl - crystal form 3”. X-ray diffraction, 1 ligand (ANP), 20 pockets (best druggability 0.79). MolNFT v1 #113599 on GenesisL1: 3D structure, binding…
- PDB
- 5AKD
- Type
- protein
- Length
- 5,688 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA mismatch repair protein muts; DNA mismatch repair protein mutl
- UniProt
- P23909, P23367
- Ligands
- ANP
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, I, J | DNA mismatch repair protein muts | protein | 663 | 49% helix, 18% strand | P23909 |
| C, D, G, H, K, L | DNA mismatch repair protein mutl | protein | 285 | 38% helix, 26% strand | P23367 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 6 copies · chains A, B, E, F, I, J
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 | 460 | 0.79 | 0.87 | 67 | ANP |
| 2 | 849 | 0.79 | 0.82 | 92 | empty |
| 3 | 118 | 0.79 | 0.97 | 30 | empty |
| 4 | 115 | 0.79 | 0.97 | 25 | empty |
| 5 | 119 | 0.78 | 0.96 | 26 | empty |
Interfaces
17 interfaces between chains.
- E–F · 3081 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 3047 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 3016 Ų buried · 19 hydrogen bonds · protein-protein
- D–G · 1295 Ų buried · 5 hydrogen bonds · protein-protein
- H–L · 1243 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5AKD · MutS in complex with the N-terminal domain of MutL - crystal form 3 · 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 P23909
- Every structure of UniProt P23367
- Elsewhere: RCSB PDB 5AKD · PDBe 5AKD · UniProt P23909 · UniProt P23367
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