MolNFT v1 · #70225 · protein
Crystal structure of mycobacterium tuberculosis pantothenate synthetase at 1.70 ångström resolution in complex with 2-(2- ((benzofuran-2-CARBOXAMIDO)METHYL)-5-methoxy-1H-indol-1-YL)ACETIC acid
3LE8: “Crystal structure of mycobacterium tuberculosis pantothenate synthetase at 1.70 ångström resolution in…”. X-ray diffraction, 1 ligand (2B5), 4 pockets (best druggability 0.83). MolNFT v1 #70225 on GenesisL1: 3D structure, binding…
- PDB
- 3LE8
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate synthetase
- EC
- 6.3.2.1
- UniProt
- P0A5R0
- Ligands
- 2B5
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate synthetase (EC 6.3.2.1) | protein | 288 | 42% helix, 22% strand | P0A5R0 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 276 | 41% helix, 24% strand | P0A5R0 |
Ligands and binding sites
- 2B5 · 2-(2-((benzofuran-2-carboxamido)methyl)-5-methoxy-1H-indol-1-yl)acetic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- EOH · Ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.83 | 0.89 | 65 | 2B5 |
| 2 | 447 | 0.79 | 0.87 | 51 | 2B5 |
| 3 | 325 | 0.67 | 0.82 | 27 | GOL |
| 4 | 65 | 0.32 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1204 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3LE8 · Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.70 Angstrom… · the same entry in another collection · chain B against B, 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 P0A5R0
- Elsewhere: RCSB PDB 3LE8 · PDBe 3LE8 · UniProt P0A5R0
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