Research workbench
Human metallo beta lactamase domain containing protein 1 (HMBLAC1)
Analyse Human metallo beta lactamase domain containing protein 1 (HMBLAC1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V0H
- Type
- protein
- Length
- 885 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase domain-containing protein 1 1
- EC
- 3.-.-.-
- UniProt
- A4D2B0
- Ligands
- FE
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase domain-containing protein 1 1 (EC 3.-.-.-) | protein | 220 | 20% helix, 35% strand | A4D2B0 |
| B, C | Metallo-beta-lactamase domain-containing protein 1 1 (EC 3.-.-.-) | protein | 221 | 22% helix, 35% strand | A4D2B0 |
| D | Metallo-beta-lactamase domain-containing protein 1 1 (EC 3.-.-.-) | protein | 223 | 20% helix, 35% strand | A4D2B0 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.65 | 0.78 | 57 | empty |
| 2 | 298 | 0.63 | 0.80 | 36 | empty |
| 3 | 171 | 0.49 | 0.77 | 22 | empty |
| 4 | 101 | 0.35 | 0.73 | 21 | empty |
| 5 | 57 | 0.34 | 0.78 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–D · 300 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 272 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 269 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 249 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4V0H · Human metallo beta lactamase domain containing protein 1 (hMBLAC1) · the same entry in another collection · chain A against A, TM-score 1.00
- A4D2B0 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase domain- containing protein 1… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 A4D2B0
- Elsewhere: RCSB PDB 4V0H · PDBe 4V0H · UniProt A4D2B0
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