MolNFT v1 · #101442 · protein
Crystal structure of a putative gdsl-like lipase (BACOVA_04955) from bacteroides ovatus atcc 8483 at 2.10 a resolution
4NRD · Uncharacterized protein: “Crystal structure of a putative gdsl-like lipase (BACOVA_04955) from bacteroides ovatus atcc 8483 at 2.10 a…”. X-ray diffraction, 10 pockets (best druggability 0.72). MolNFT v1 #101442 on GenesisL1: 3D…
- PDB
- 4NRD
- Type
- protein
- Length
- 1,240 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A7M4B4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F | Uncharacterized protein | protein | 207 | 36% helix, 16% strand | A7M4B4 |
| B, E | Uncharacterized protein | protein | 206 | 36% helix, 17% strand | A7M4B4 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.72 | 0.79 | 62 | empty |
| 2 | 649 | 0.71 | 0.79 | 64 | empty |
| 3 | 293 | 0.51 | 0.74 | 40 | empty |
| 4 | 158 | 0.47 | 0.77 | 21 | empty |
| 5 | 153 | 0.46 | 0.76 | 24 | empty |
Interfaces
7 interfaces between chains.
- D–F · 695 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 677 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 675 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 671 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 669 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 4NRD · Crystal structure of a putative GDSL-like lipase (BACOVA_04955) from Bacteroides ovatus… · 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 A7M4B4
- Elsewhere: RCSB PDB 4NRD · PDBe 4NRD · UniProt A7M4B4
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