MolNFT v1 · #156556 · protein
Dehydratase, nisb, bound to a non-eliminable substrate analog
6M7Y · Nisin biosynthesis protein nisb: “Dehydratase, nisb, bound to a non-eliminable substrate analog”. X-ray diffraction, 1 ligand (J9A), 20 pockets (best druggability 0.80). MolNFT v1 #156556 on GenesisL1: 3D structure, binding sites…
- PDB
- 6M7Y
- Type
- protein
- Length
- 1,930 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nisin biosynthesis protein nisb; Lantibiotic
- UniProt
- P20103, Q7BB86
- Ligands
- J9A
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nisin biosynthesis protein nisb | protein | 952 | 45% helix, 20% strand | P20103 |
| B | Nisin biosynthesis protein nisb | protein | 948 | 46% helix, 21% strand | P20103 |
| C, D | Lantibiotic | protein | 15 | 0% helix, 20% strand | Q7BB86 |
Ligands and binding sites
- J9A · N-[(2S)-2-amino-2-carboxyethyl]-L-alpha-glutamine · ligand · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.80 | 0.85 | 72 | J9A |
| 2 | 610 | 0.80 | 0.85 | 67 | J9A |
| 3 | 778 | 0.76 | 0.80 | 68 | empty |
| 4 | 550 | 0.75 | 0.82 | 54 | empty |
| 5 | 604 | 0.75 | 0.81 | 62 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3229 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 770 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 760 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 324 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 307 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 26 modified, 4 covalent, 2 disulfide (engineered, covalent ligand, disulfide).
Compared structures
- 6M7Y · Dehydratase, NisB, bound to a non-eliminable substrate analog · the same entry in another collection · chain D against D, TM-score 1.00
- P20103 · AlphaFold monomer V2.0 prediction for nisin biosynthesis protein nisb (P20103) · a predicted model of the same protein · chain B 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 P20103
- Every structure of UniProt Q7BB86
- Elsewhere: RCSB PDB 6M7Y · PDBe 6M7Y · UniProt P20103 · UniProt Q7BB86
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