Research workbench
Crystal structure of N-terminally truncated ndm-1 metallo-beta- lactamase
Analyse Crystal structure of N-terminally truncated ndm-1 metallo-beta- lactamase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TWT
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo beta lactamase ndm-1
- UniProt
- E9NWK5
- Ligands
- CA, ZN, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo beta lactamase ndm-1 | protein | 224 | 26% helix, 28% strand | E9NWK5 |
| B | Metallo beta lactamase ndm-1 | protein | 228 | 24% helix, 31% strand | E9NWK5 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.78 | 0.97 | 21 | empty |
| 2 | 76 | 0.44 | 0.81 | 19 | empty |
| 3 | 119 | 0.39 | 0.75 | 25 | empty |
| 4 | 74 | 0.31 | 0.74 | 21 | empty |
| 5 | 54 | 0.30 | 0.75 | 15 | CL |
Interfaces
1 interface between chains.
- A–B · 913 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6TWT · Crystal structure of N-terminally truncated NDM-1 metallo-beta-lactamase · 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 6TWT · PDBe 6TWT · UniProt E9NWK5
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