Research workbench
Crystal structure of the M. tuberculosis sulfate ester dioxygenase RV3406 in complex with iron.
Analyse Crystal structure of the M. tuberculosis sulfate ester dioxygenase RV3406 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CVY
- Type
- protein
- Length
- 951 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dioxygenase RV3406/MT3514
- EC
- 1.-.-.-
- UniProt
- P65075
- Ligands
- FE, NO3
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dioxygenase RV3406/MT3514 (EC 1.-.-.-) | protein | 240 | 23% helix, 31% strand | P65075 |
| B | Dioxygenase RV3406/MT3514 (EC 1.-.-.-) | protein | 240 | 23% helix, 31% strand | P65075 |
| C | Dioxygenase RV3406/MT3514 (EC 1.-.-.-) | protein | 236 | 25% helix, 31% strand | P65075 |
| D | Dioxygenase RV3406/MT3514 (EC 1.-.-.-) | protein | 235 | 24% helix, 31% strand | P65075 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.89 | 0.91 | 83 | empty |
| 2 | 300 | 0.62 | 0.80 | 54 | empty |
| 3 | 172 | 0.53 | 0.79 | 25 | empty |
| 4 | 160 | 0.52 | 0.79 | 24 | empty |
| 5 | 123 | 0.45 | 0.77 | 24 | FE |
Interfaces
6 interfaces between chains.
- A–B · 1006 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1001 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 837 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 819 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 291 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4CVY · Crystal structure of the M. tuberculosis sulfate ester dioxygenase Rv3406 in complex with… · 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 P65075
- Elsewhere: RCSB PDB 4CVY · PDBe 4CVY · UniProt P65075
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