MolNFT v1 · #65039 · protein
Crystal structure of the effector binding domain of a catm variant (R156H)
3GLB · Hth-type transcriptional regulator catm: “Crystal structure of the effector binding domain of a catm variant (R156H)”. X-ray diffraction, 2 ligands (CCU, SO4), 11 pockets (best druggability 0.79). MolNFT v1 #65039 on GenesisL1: 3D…
- PDB
- 3GLB
- Type
- protein
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional regulator catm
- UniProt
- P07774
- Ligands
- CCU, SO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional regulator catm | protein | 215 | 35% helix, 28% strand | P07774 |
| B | Hth-type transcriptional regulator catm | protein | 212 | 37% helix, 28% strand | P07774 |
| C | Hth-type transcriptional regulator catm | protein | 212 | 33% helix, 28% strand | P07774 |
| D | Hth-type transcriptional regulator catm | protein | 219 | 31% helix, 27% strand | P07774 |
Ligands and binding sites
- CCU · (2Z,4Z)-hexa-2,4-dienedioic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains B
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.79 | 0.81 | 89 | empty |
| 2 | 144 | 0.65 | 0.87 | 26 | CCU |
| 3 | 151 | 0.63 | 0.86 | 27 | CCU, SO4 |
| 4 | 149 | 0.62 | 0.85 | 25 | CCU, GOL |
| 5 | 138 | 0.62 | 0.86 | 24 | CCU |
Interfaces
4 interfaces between chains.
- C–D · 1449 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1403 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 640 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 41 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3GLB · Crystal structure of the effector binding domain of a CATM variant (R156H) · the same entry in another collection · chain D against D, TM-score 1.00
- P07774 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator catm (P07774) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P07774
- Elsewhere: RCSB PDB 3GLB · PDBe 3GLB · UniProt P07774
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