MolNFT v1 · #105657 · protein + DNA
Crystal structure of a nanog homeobox (nanog) from homo sapiens at 3.30 a resolution
4RBO · Putative homeobox protein NANOGP8: “Crystal structure of a nanog homeobox (nanog) from homo sapiens at 3.30 a resolution”. X-ray diffraction, 9 pockets (best druggability 0.52). MolNFT v1 #105657 on GenesisL1: 3D structure, binding…
- PDB
- 4RBO
- Type
- protein + DNA
- Length
- 157 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative homeobox protein NANOGP8; 5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3'…
- UniProt
- Q6NSW7
- Pockets
- 9 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative homeobox protein NANOGP8 | protein | 55 | 73% helix, 0% strand | Q6NSW7 |
| B, E | 5'-D(*GP*GP*CP*CP*CP*AP*TP*TP*CP*AP*AP*G)-3' | dna | 12 | — | — |
| C, F | 5'-D(*CP*TP*TP*GP*AP*AP*TP*GP*GP*GP*CP*C)-3' | dna | 12 | — | — |
| D | Putative homeobox protein NANOGP8 | protein | 54 | 74% helix, 0% strand | Q6NSW7 |
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.52 | 0.80 | 15 | empty |
| 2 | 128 | 0.48 | 0.79 | 14 | empty |
| 3 | 153 | 0.47 | 0.77 | 21 | empty |
| 4 | 126 | 0.46 | 0.78 | 18 | empty |
| 5 | 99 | 0.45 | 0.80 | 14 | empty |
Interfaces
11 interfaces between chains.
- B–C · 532 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- E–F · 505 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–B · 371 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–E · 345 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–F · 330 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 4RBO · Crystal structure of a Nanog homeobox (NANOG) from Homo sapiens at 3.30 A resolution · the same entry in another collection · chain F against F, TM-score 1.00
- Q6NSW7 · AlphaFold monomer V2.0 prediction for homeobox protein NANOGP8 (Q6NSW7) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q6NSW7
- Elsewhere: RCSB PDB 4RBO · PDBe 4RBO · UniProt Q6NSW7
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