Research workbench
Crystal structure of mannitol dehydrogenase (chmdh) from cladosporium herbarum in complex with NADP+ and na
Analyse Crystal structure of mannitol dehydrogenase (chmdh) from cladosporium herbarum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KRG
- Type
- protein
- Length
- 2,128 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP-dependent mannitol dehydrogenase
- EC
- 1.1.1.138
- UniProt
- P0C0Y5
- Ligands
- NAP, NA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, H | NADP-dependent mannitol dehydrogenase (EC 1.1.1.138) | protein | 266 | 47% helix, 14% strand | P0C0Y5 |
| B, E | NADP-dependent mannitol dehydrogenase (EC 1.1.1.138) | protein | 265 | 47% helix, 14% strand | P0C0Y5 |
| F | NADP-dependent mannitol dehydrogenase (EC 1.1.1.138) | protein | 270 | 46% helix, 14% strand | P0C0Y5 |
| G | NADP-dependent mannitol dehydrogenase (EC 1.1.1.138) | protein | 264 | 47% helix, 14% strand | P0C0Y5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 4 copies · chains A, C, B, D, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.85 | 0.86 | 62 | NA |
| 2 | 819 | 0.77 | 0.80 | 85 | NAP |
| 3 | 428 | 0.75 | 0.85 | 55 | NAP |
| 4 | 381 | 0.75 | 0.86 | 56 | NAP |
| 5 | 451 | 0.74 | 0.84 | 59 | NAP |
Interfaces
11 interfaces between chains.
- A–D · 2203 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 2199 Ų buried · 46 hydrogen bonds · protein-protein
- F–H · 1732 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1725 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1710 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7KRG · Crystal Structure of Mannitol Dehydrogenase (ChMDH) from Cladosporium herbarum in complex… · the same entry in another collection · chain H against H, TM-score 1.00
- P0C0Y5 · AlphaFold monomer V2.0 prediction for NADP-dependent mannitol dehydrogenase (P0C0Y5) · a predicted model of the same protein · chain G 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 P0C0Y5
- Elsewhere: RCSB PDB 7KRG · PDBe 7KRG · UniProt P0C0Y5
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