Research workbench
Crystal structure of the new deli metallo beta lactamase variant 5 from klebsiella pneumoniae
Analyse Crystal structure of the new deli metallo beta lactamase variant 5 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MGY
- Type
- protein
- Length
- 923 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase ndm-5
- UniProt
- U5TTL2
- Ligands
- ZN, K
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase ndm-5 | protein | 230 | 26% helix, 30% strand | U5TTL2 |
| B | Metallo-beta-lactamase ndm-5 | protein | 226 | 26% helix, 29% strand | U5TTL2 |
| C | Metallo-beta-lactamase ndm-5 | protein | 238 | 26% helix, 31% strand | U5TTL2 |
| D | Metallo-beta-lactamase ndm-5 | protein | 229 | 27% helix, 33% strand | U5TTL2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- K · Potassium ion · metal · 2 copies · chains A, D, B, C
- GOL · Glycerol · additive · chains B
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 | 106 | 0.78 | 0.98 | 21 | empty |
| 2 | 112 | 0.77 | 0.96 | 23 | empty |
| 3 | 131 | 0.50 | 0.80 | 28 | empty |
| 4 | 86 | 0.40 | 0.78 | 20 | empty |
| 5 | 149 | 0.40 | 0.74 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1032 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1026 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 419 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 158 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6MGY · Crystal Structure of the New Deli Metallo Beta Lactamase Variant 5 from Klebsiella… · 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 U5TTL2
- Elsewhere: RCSB PDB 6MGY · PDBe 6MGY · UniProt U5TTL2
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