MolNFT v1 · #100296 · protein + DNA
Zinc uptake regulator complexed with zinc and DNA
4MTD · Zinc uptake regulation protein: “Zinc uptake regulator complexed with zinc and DNA”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.68). MolNFT v1 #100296 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4MTD
- Type
- protein + DNA
- Length
- 664 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc uptake regulation protein; Znuabc operator DNA
- UniProt
- P0AC51
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc uptake regulation protein | protein | 149 | 48% helix, 20% strand | P0AC51 |
| B | Zinc uptake regulation protein | protein | 150 | 48% helix, 21% strand | P0AC51 |
| C | Zinc uptake regulation protein | protein | 148 | 50% helix, 22% strand | P0AC51 |
| D | Zinc uptake regulation protein | protein | 151 | 46% helix, 21% strand | P0AC51 |
| Y | Znuabc operator DNA | dna | 33 | — | — |
| Z | Znuabc operator DNA | dna | 33 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.68 | 0.77 | 82 | empty |
| 2 | 647 | 0.65 | 0.75 | 69 | empty |
| 3 | 274 | 0.59 | 0.79 | 32 | empty |
| 4 | 52 | 0.58 | 0.91 | 17 | empty |
| 5 | 201 | 0.44 | 0.74 | 25 | empty |
Interfaces
12 interfaces between chains.
- A–D · 1440 Ų buried · 20 hydrogen bonds · protein-protein
- Y–Z · 1414 Ų buried · 118 hydrogen bonds · nucleic-nucleic
- B–C · 1407 Ų buried · 16 hydrogen bonds · protein-protein
- D–Y · 476 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–Y · 474 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
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 P0AC51
- Elsewhere: RCSB PDB 4MTD · PDBe 4MTD · UniProt P0AC51
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