MolNFT v1 · #17380 · protein
Crystal structure of cdp-tyvelose 2-epimerase complexed with NAD and cdp
1ORR · Cdp-tyvelose-2-epimerase: “Crystal structure of cdp-tyvelose 2-epimerase complexed with NAD and cdp”. X-ray diffraction, 2 ligands (NAD, CDP), 11 pockets (best druggability 0.85). MolNFT v1 #17380 on GenesisL1: 3D structure, binding…
- PDB
- 1ORR
- Type
- protein
- Length
- 1,347 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cdp-tyvelose-2-epimerase
- EC
- 5.1.3.-
- UniProt
- P14169
- Ligands
- NAD, CDP
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cdp-tyvelose-2-epimerase (EC 5.1.3.-) | protein | 338 | 45% helix, 20% strand | P14169 |
| C | Cdp-tyvelose-2-epimerase (EC 5.1.3.-) | protein | 335 | 45% helix, 20% strand | P14169 |
| D | Cdp-tyvelose-2-epimerase (EC 5.1.3.-) | protein | 336 | 45% helix, 20% strand | P14169 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- CDP · Cytidine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
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 | 882 | 0.85 | 0.88 | 71 | empty |
| 2 | 1019 | 0.85 | 0.86 | 85 | NAD, CDP |
| 3 | 1130 | 0.84 | 0.85 | 89 | NAD, CDP |
| 4 | 1078 | 0.84 | 0.85 | 85 | NAD, CDP |
| 5 | 1158 | 0.83 | 0.84 | 94 | NAD, CDP |
Interfaces
6 interfaces between chains.
- B–D · 1278 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1271 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 735 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 694 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 66 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1ORR · Crystal Structure of CDP-Tyvelose 2-Epimerase complexed with NAD and CDP · the same entry in another collection · chain A against A, TM-score 1.00
- P14169 · AlphaFold monomer V2.0 prediction for cdp-paratose 2-epimerase (P14169) · a predicted model of the same protein · 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 P14169
- Elsewhere: RCSB PDB 1ORR · PDBe 1ORR · UniProt P14169
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