MolNFT v1 · #88474 · protein
Crystal structure of the M. tuberculosis sulfate ester dioxygenase RV3406 in complex with iron.
4CVY · Dioxygenase RV3406/MT3514: “Crystal structure of the M. tuberculosis sulfate ester dioxygenase RV3406 in complex with iron.”. X-ray diffraction, 2 ligands (FE, NO3), 12 pockets (best druggability 0.89). MolNFT v1 #88474 on…
- 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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