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Gim-1-3MOL native. crystal structures of pseudomonas aeruginosa gim-1: active site plasticity in metallo-beta-lactamases
Analyse Gim-1-3MOL native. crystal structures of pseudomonas aeruginosa gim-1: active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YNT
- Type
- protein
- Length
- 661 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gim-1 protein
- UniProt
- Q704V1
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gim-1 protein | protein | 221 | 26% helix, 31% strand | Q704V1 |
| B | Gim-1 protein | protein | 219 | 28% helix, 31% strand | Q704V1 |
| C | Gim-1 protein | protein | 221 | 27% helix, 31% strand | Q704V1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.71 | 0.78 | 71 | empty |
| 2 | 348 | 0.62 | 0.78 | 54 | empty |
| 3 | 93 | 0.38 | 0.76 | 17 | empty |
| 4 | 52 | 0.26 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 782 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 726 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 363 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2YNT · GIM-1-3Mol native. Crystal structures of Pseudomonas aeruginosa GIM- 1: active site… · the same entry in another collection · chain B against B, 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 Q704V1
- Elsewhere: RCSB PDB 2YNT · PDBe 2YNT · UniProt Q704V1
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