MolNFT v1 · #64082 · protein
Structure of tetrahydrodipicolinate N-succinyltransferase (RV1201C;DAPD) in complex with succinyl-CoA from mycobacterium tuberculosis
3FSY: “Structure of tetrahydrodipicolinate N-succinyltransferase (RV1201C;DAPD) in complex with succinyl-CoA from…”. X-ray diffraction, 3 ligands (SCA, MG, NA), 9 pockets (best druggability 0.78). MolNFT v1 #64082 on GenesisL1: 3D…
- PDB
- 3FSY
- Type
- protein
- Length
- 1,517 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrahydrodipicolinate N-succinyltransferase
- EC
- 2.3.1.117
- UniProt
- O05302
- Ligands
- SCA, MG, NA
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117) | protein | 304 | 13% helix, 34% strand | O05302 |
| B | Tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117) | protein | 307 | 13% helix, 33% strand | O05302 |
| C | Tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117) | protein | 297 | 14% helix, 34% strand | O05302 |
| D | Tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117) | protein | 308 | 13% helix, 33% strand | O05302 |
| E | Tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117) | protein | 301 | 14% helix, 33% strand | O05302 |
Ligands and binding sites
- SCA · Succinyl-coenzyme A · ligand · 4 copies · chains A, B, D, C, E
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.78 | 0.84 | 98 | empty |
| 2 | 266 | 0.74 | 0.88 | 52 | MG |
| 3 | 701 | 0.70 | 0.77 | 81 | ACY |
| 4 | 385 | 0.70 | 0.82 | 66 | SCA |
| 5 | 329 | 0.57 | 0.76 | 45 | SCA |
Interfaces
6 interfaces between chains.
- B–C · 1787 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1787 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1625 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 419 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 221 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3FSY · Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c;DapD) 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 O05302
- Elsewhere: RCSB PDB 3FSY · PDBe 3FSY · UniProt O05302
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