MolNFT v2 · #127081 · protein
X-ray generated oxyferrous complex of DtpA from Streptomyces lividans
5MAP: “X-ray generated oxyferrous complex of DtpA from Streptomyces lividans”. X-ray diffraction at 1.49, 2 ligands (HEM, OXY), 12 pockets (best druggability 0.84). MolNFT v2 #127081 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5MAP
- Type
- protein
- Length
- 736 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.49
- Source
- Streptomyces lividans TK24
- Molecule
- DtpA
- UniProt
- A0A076MAJ9
- Ligands
- HEM, OXY
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.49 · 2 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DtpA | protein | 367 | 29% helix, 23% strand | A0A076MAJ9 |
| B | DtpA | protein | 369 | 27% helix, 23% strand | A0A076MAJ9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.84 | 0.93 | 45 | HEM, OXY |
| 2 | 352 | 0.81 | 0.91 | 50 | HEM, OXY |
| 3 | 361 | 0.60 | 0.77 | 44 | empty |
| 4 | 339 | 0.59 | 0.77 | 45 | empty |
| 5 | 119 | 0.51 | 0.82 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2714 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 5MAP · X-ray generated oxyferrous complex of dtpa from streptomyces lividans · the same entry in another collection · 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 A0A076MAJ9
- Elsewhere: RCSB PDB 5MAP · PDBe 5MAP · UniProt A0A076MAJ9
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