MolNFT v1 · #158435 · protein
Crystal structure of beta-barrel-like protein of domain of unknown function DUF1849 from brucella abortus
6NTR · ATP/GTP-binding site-containing protein a: “Crystal structure of beta-barrel-like protein of domain of unknown function DUF1849 from brucella abortus”. X-ray diffraction, 10 pockets (best druggability 0.83). MolNFT v1 #158435 on…
- PDB
- 6NTR
- Type
- protein
- Length
- 957 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP/GTP-binding site-containing protein a
- UniProt
- A0A0M1WBA0
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP/GTP-binding site-containing protein a | protein | 241 | 10% helix, 58% strand | A0A0M1WBA0 |
| B | ATP/GTP-binding site-containing protein a | protein | 238 | 8% helix, 57% strand | A0A0M1WBA0 |
| C | ATP/GTP-binding site-containing protein a | protein | 242 | 9% helix, 56% strand | A0A0M1WBA0 |
| D | ATP/GTP-binding site-containing protein a | protein | 236 | 8% helix, 56% strand | A0A0M1WBA0 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.83 | 0.85 | 66 | EDO |
| 2 | 777 | 0.83 | 0.85 | 58 | EDO |
| 3 | 782 | 0.82 | 0.85 | 58 | EDO |
| 4 | 821 | 0.82 | 0.84 | 64 | GOL, EDO |
| 5 | 569 | 0.64 | 0.75 | 66 | empty |
Interfaces
5 interfaces between chains.
- C–D · 671 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 370 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 243 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 243 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 6NTR · Crystal Structure of Beta-barrel-like Protein of Domain of Unknown Function DUF1849 from… · 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 A0A0M1WBA0
- Elsewhere: RCSB PDB 6NTR · PDBe 6NTR · UniProt A0A0M1WBA0
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