Research workbench
Crystal structure of a metagenomic short-chain oxidoreductase (sdr) in complex with NADP
Analyse Crystal structure of a metagenomic short-chain oxidoreductase (sdr) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RKR
- Type
- protein
- Length
- 888 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain oxidoreductase
- EC
- 1.1.1.100
- UniProt
- B2BKB1
- Ligands
- NAP, SO4
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short chain oxidoreductase (EC 1.1.1.100) | protein | 221 | 48% helix, 18% strand | B2BKB1 |
| B | Short chain oxidoreductase (EC 1.1.1.100) | protein | 221 | 48% helix, 16% strand | B2BKB1 |
| C | Short chain oxidoreductase (EC 1.1.1.100) | protein | 224 | 48% helix, 16% strand | B2BKB1 |
| D | Short chain oxidoreductase (EC 1.1.1.100) | protein | 222 | 46% helix, 17% strand | B2BKB1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 13 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.67 | 0.88 | 30 | empty |
| 2 | 337 | 0.58 | 0.76 | 44 | SO4 |
| 3 | 328 | 0.57 | 0.76 | 48 | NAP, SO4 |
| 4 | 252 | 0.55 | 0.77 | 32 | NAP, SO4 |
| 5 | 227 | 0.54 | 0.78 | 31 | SO4 |
Interfaces
4 interfaces between chains.
- B–C · 1576 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1359 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 485 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 75 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3RKR · Crystal structure of a metagenomic short-chain oxidoreductase (SDR) in complex with NADP · 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 B2BKB1
- Elsewhere: RCSB PDB 3RKR · PDBe 3RKR · UniProt B2BKB1
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