Research workbench
Mycobacterium abscessus nadd in complex with nicotinic acid adenine dinucleotide
Analyse Mycobacterium abscessus nadd in complex with nicotinic acid adenine dinucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DEO
- Type
- protein
- Length
- 728 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate-nucleotide adenylyltransferase
- EC
- 2.7.7.18
- UniProt
- B1MMZ4
- Ligands
- DND
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) | protein | 189 | 41% helix, 21% strand | B1MMZ4 |
| B | Nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) | protein | 179 | 42% helix, 21% strand | B1MMZ4 |
| C | Nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) | protein | 180 | 41% helix, 20% strand | B1MMZ4 |
| D | Nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) | protein | 180 | 40% helix, 19% strand | B1MMZ4 |
Ligands and binding sites
- DND · Nicotinic acid adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.81 | 0.82 | 89 | empty |
| 2 | 373 | 0.65 | 0.80 | 50 | DND |
| 3 | 300 | 0.65 | 0.81 | 44 | DND |
| 4 | 317 | 0.63 | 0.80 | 47 | DND |
| 5 | 316 | 0.63 | 0.80 | 48 | DND |
Interfaces
4 interfaces between chains.
- A–B · 1039 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1030 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 639 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 609 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5DEO · Mycobacterium abscessus NadD in complex with nicotinic acid adenine dinucleotide · 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 B1MMZ4
- Elsewhere: RCSB PDB 5DEO · PDBe 5DEO · UniProt B1MMZ4
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