MolNFT v1 · #71005 · protein
The crystal structure of a short-chain dehydrogenase from streptomyces avermitilis to 2A
3M1A · Putative dehydrogenase: “The crystal structure of a short-chain dehydrogenase from streptomyces avermitilis to 2A”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.88). MolNFT v1 #71005 on GenesisL1: 3D structure…
- PDB
- 3M1A
- Type
- protein
- Length
- 2,703 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dehydrogenase
- UniProt
- Q82PV2
- Ligands
- NA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 10 distinct chains · 54% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative dehydrogenase | protein | 270 | 53% helix, 17% strand | Q82PV2 |
| B | Putative dehydrogenase | protein | 271 | 55% helix, 18% strand | Q82PV2 |
| C | Putative dehydrogenase | protein | 272 | 53% helix, 17% strand | Q82PV2 |
| D | Putative dehydrogenase | protein | 275 | 52% helix, 17% strand | Q82PV2 |
| E | Putative dehydrogenase | protein | 271 | 54% helix, 18% strand | Q82PV2 |
| F | Putative dehydrogenase | protein | 268 | 54% helix, 17% strand | Q82PV2 |
| G | Putative dehydrogenase | protein | 272 | 53% helix, 18% strand | Q82PV2 |
| H | Putative dehydrogenase | protein | 268 | 56% helix, 17% strand | Q82PV2 |
| I | Putative dehydrogenase | protein | 269 | 55% helix, 19% strand | Q82PV2 |
| J | Putative dehydrogenase | protein | 267 | 55% helix, 17% strand | Q82PV2 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, C, B, D, E
- ACT · Acetate ion · additive · 2 copies · chains D, E, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.88 | 0.90 | 124 | empty |
| 2 | 1198 | 0.88 | 0.90 | 128 | NA |
| 3 | 1185 | 0.88 | 0.89 | 126 | NA |
| 4 | 544 | 0.84 | 0.90 | 63 | empty |
| 5 | 708 | 0.83 | 0.87 | 70 | empty |
Interfaces
20 interfaces between chains.
- A–B · 3926 Ų buried · 68 hydrogen bonds · protein-protein
- G–I · 3796 Ų buried · 61 hydrogen bonds · protein-protein
- C–F · 3793 Ų buried · 63 hydrogen bonds · protein-protein
- H–J · 3758 Ų buried · 67 hydrogen bonds · protein-protein
- D–E · 3731 Ų buried · 64 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3M1A · The Crystal Structure of a Short-chain Dehydrogenase from Streptomyces avermitilis to 2A · 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 Q82PV2
- Elsewhere: RCSB PDB 3M1A · PDBe 3M1A · UniProt Q82PV2
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