Research workbench
Structure of ndm-1 in complex with macrocycle inhibitor NDM1I-1F
Analyse Structure of ndm-1 in complex with macrocycle inhibitor NDM1I-1F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XBE
- Type
- protein
- Length
- 948 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blandm-4_1_JQ348841; Macrocycle inhibitor NDM1I-1F
- UniProt
- E9NWK5
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Blandm-4_1_JQ348841 | protein | 229 | 26% helix, 31% strand | E9NWK5 |
| F, G, H, I | Macrocycle inhibitor NDM1I-1F | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, F, B, G, C, H, D, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.78 | 0.97 | 20 | empty |
| 2 | 985 | 0.71 | 0.75 | 75 | empty |
| 3 | 110 | 0.59 | 0.86 | 31 | empty |
| 4 | 117 | 0.50 | 0.81 | 31 | empty |
| 5 | 75 | 0.44 | 0.81 | 18 | empty |
Interfaces
8 interfaces between chains.
- B–C · 920 Ų buried · 12 hydrogen bonds · protein-protein
- C–H · 481 Ų buried · 3 hydrogen bonds · protein-protein
- B–G · 439 Ų buried · 3 hydrogen bonds · protein-protein
- D–I · 415 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 392 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 d-amino (D-amino acid).
Compared structures
- 6XBE · Structure of NDM-1 in complex with macrocycle inhibitor NDM1i-1F · 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 E9NWK5
- Elsewhere: RCSB PDB 6XBE · PDBe 6XBE · UniProt E9NWK5
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