MolNFT v1 · #184727 · protein
Crystal structure of S.POMBE MDB1 brct domains in complex with a H2A phosphopeptide
7P0L · DNA damage response protein MDB1: “Crystal structure of S.POMBE MDB1 brct domains in complex with a H2A phosphopeptide”. X-ray diffraction, 3 pockets (best druggability 0.62). MolNFT v1 #184727 on GenesisL1: 3D structure, binding…
- PDB
- 7P0L
- Type
- protein
- Length
- 401 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage response protein MDB1; Histone H2A-beta
- UniProt
- O14079, P04910
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA damage response protein MDB1 | protein | 195 | 41% helix, 16% strand | O14079 |
| C | Histone H2A-beta | protein | 6 | 0% helix, 17% strand | P04910 |
| D | Histone H2A-beta | protein | 5 | 0% helix, 20% strand | P04910 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.62 | 0.82 | 32 | empty |
| 2 | 99 | 0.36 | 0.74 | 14 | empty |
| 3 | 57 | 0.26 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 537 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 454 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 449 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 7P0L · Crystal structure of S.pombe Mdb1 BRCT domains in complex with a H2A phosphopeptide · the same entry in another collection · chain A against A, TM-score 1.00
- O14079 · AlphaFold monomer V2.0 prediction for DNA damage response protein MDB1 (O14079) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P04910 · AlphaFold monomer V2.0 prediction for histone H2A-beta (P04910) · a predicted model of the same protein · chain D against A, TM-score 0.88
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 O14079
- Every structure of UniProt P04910
- Elsewhere: RCSB PDB 7P0L · PDBe 7P0L · UniProt O14079 · UniProt P04910
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