Research workbench
Crystal structure maba bound to NADPH from M. smegmatis
Analyse Crystal structure maba bound to NADPH from M. smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OVK
- Type
- protein
- Length
- 928 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] reductase fabg
- EC
- 1.1.1.100
- UniProt
- P71534
- Ligands
- NDP
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acyl-carrier-protein] reductase fabg (EC 1.1.1.100) | protein | 242 | 47% helix, 16% strand | P71534 |
| B | 3-oxoacyl-[acyl-carrier-protein] reductase fabg (EC 1.1.1.100) | protein | 229 | 45% helix, 18% strand | P71534 |
| C | 3-oxoacyl-[acyl-carrier-protein] reductase fabg (EC 1.1.1.100) | protein | 227 | 44% helix, 18% strand | P71534 |
| D | 3-oxoacyl-[acyl-carrier-protein] reductase fabg (EC 1.1.1.100) | protein | 230 | 45% helix, 17% strand | P71534 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.71 | 0.99 | 25 | empty |
| 2 | 50 | 0.70 | 0.98 | 23 | empty |
| 3 | 616 | 0.69 | 0.77 | 64 | NDP |
| 4 | 310 | 0.61 | 0.78 | 36 | NDP |
| 5 | 262 | 0.59 | 0.79 | 40 | NDP |
Interfaces
6 interfaces between chains.
- C–D · 1951 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1950 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1942 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1935 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 538 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5OVK · Crystal structure MabA bound to NADPH from M. smegmatis · the same entry in another collection · chain D against D, TM-score 1.00
- P71534 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] reductase maba… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P71534
- Elsewhere: RCSB PDB 5OVK · PDBe 5OVK · UniProt P71534
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