Research workbench
Crystal structure of human MRE11: understanding tumorigenic mutations
Analyse Crystal structure of human MRE11: understanding tumorigenic mutations in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T1I
- Type
- protein
- Length
- 1,517 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double-strand break repair protein MRE11A
- UniProt
- P49959
- Ligands
- MN
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double-strand break repair protein MRE11A | protein | 376 | 25% helix, 26% strand | P49959 |
| B | Double-strand break repair protein MRE11A | protein | 378 | 25% helix, 26% strand | P49959 |
| C | Double-strand break repair protein MRE11A | protein | 377 | 25% helix, 26% strand | P49959 |
| D | Double-strand break repair protein MRE11A | protein | 386 | 24% helix, 26% strand | P49959 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 15 copies · chains A, B, C, D
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.71 | 0.78 | 75 | empty |
| 2 | 517 | 0.68 | 0.78 | 64 | GOL |
| 3 | 317 | 0.67 | 0.82 | 44 | GOL |
| 4 | 345 | 0.63 | 0.79 | 31 | empty |
| 5 | 311 | 0.61 | 0.79 | 33 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1032 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 810 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 144 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 118 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 3T1I · Crystal Structure of Human Mre11: Understanding Tumorigenic Mutations · the same entry in another collection · chain D against D, TM-score 1.00
- P49959 · AlphaFold monomer V2.0 prediction for double-strand break repair protein MRE11 (P49959) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P49959
- Elsewhere: RCSB PDB 3T1I · PDBe 3T1I · UniProt P49959
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