Research workbench
Crystal structure of hmra
Analyse Crystal structure of hmra in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RAM
- Type
- protein
- Length
- 1,561 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hmra protein
- UniProt
- Q99Q45
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Hmra protein | protein | 391 | 45% helix, 21% strand | Q99Q45 |
| B | Hmra protein | protein | 389 | 45% helix, 22% strand | Q99Q45 |
| C | Hmra protein | protein | 390 | 44% helix, 22% strand | Q99Q45 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 32 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.73 | 0.80 | 59 | ZN, GOL |
| 2 | 657 | 0.73 | 0.79 | 58 | GOL |
| 3 | 613 | 0.71 | 0.79 | 61 | ZN, GOL |
| 4 | 619 | 0.70 | 0.78 | 63 | GOL |
| 5 | 137 | 0.69 | 0.90 | 30 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1035 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1022 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1013 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1000 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 413 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 23 modified (engineered).
Compared structures
- 3RAM · Crystal structure of HmrA · 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 Q99Q45
- Elsewhere: RCSB PDB 3RAM · PDBe 3RAM · UniProt Q99Q45
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