MolNFT v1 · #159421 · protein + DNA
Crystal structure of hmces srap domain in complex with palindromic 3' overhang DNA
6OOV · Embryonic stem cell-specific 5-hydroxymethylcytosine…: “Crystal structure of hmces srap domain in complex with palindromic 3' overhang DNA”. X-ray diffraction, 1 ligand (UNX), 5 pockets (best druggability 0.71). MolNFT v1 #159421 on…
- PDB
- 6OOV
- Type
- protein + DNA
- Length
- 523 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Embryonic stem cell-specific 5-hydroxymethylcytosine- binding protein; DNA…
- EC
- 3.4.-.-
- UniProt
- Q96FZ2
- Ligands
- UNX
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Embryonic stem cell-specific 5-hydroxymethylcytosine- binding protein (EC 3.4.-.-) | protein | 250 | 20% helix, 32% strand | Q96FZ2 |
| B | Embryonic stem cell-specific 5-hydroxymethylcytosine- binding protein (EC 3.4.-.-) | protein | 250 | 20% helix, 31% strand | Q96FZ2 |
| C | DNA (5'-D(*CP*AP*AP*CP*GP*TP*TP*GP*TP*TP*TP*TP*T)-3') | dna | 11 | — | — |
| D | DNA (5'-D(*CP*AP*AP*CP*GP*TP*TP*GP*TP*TP*TP*TP*T)-3') | dna | 12 | — | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 47 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.71 | 0.79 | 52 | UNX |
| 2 | 654 | 0.70 | 0.78 | 50 | UNX |
| 3 | 126 | 0.49 | 0.79 | 20 | empty |
| 4 | 88 | 0.47 | 0.81 | 16 | UNX |
| 5 | 74 | 0.37 | 0.78 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–C · 625 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 429 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 371 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–D · 249 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6OOV · Crystal structure of HMCES SRAP domain in complex with palindromic 3' overhang DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q96FZ2 · AlphaFold monomer V2.0 prediction for abasic site processing protein hmces (Q96FZ2) · a predicted model of the same protein · chain A against A, 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 Q96FZ2
- Elsewhere: RCSB PDB 6OOV · PDBe 6OOV · UniProt Q96FZ2
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