MolNFT v1 · #125136 · protein
Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei bound to L-tryptophan hydroxamate
5L03: “Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei…”. X-ray diffraction, 2 ligands (6ZB, ZN), 3 pockets (best druggability 0.82). MolNFT v1 #125136 on GenesisL1: 3D structure…
- PDB
- 5L03
- Type
- protein
- Length
- 450 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
- EC
- 4.6.1.12
- UniProt
- A0A069B2G5
- Ligands
- 6ZB, ZN
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 158 | 35% helix, 30% strand | A0A069B2G5 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 144 | 37% helix, 33% strand | A0A069B2G5 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 148 | 35% helix, 32% strand | A0A069B2G5 |
Ligands and binding sites
- 6ZB · N-hydroxy-L-tryptophanamide · ligand · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.82 | 0.94 | 48 | empty |
| 2 | 288 | 0.63 | 0.80 | 39 | ZN, 6ZB |
| 3 | 169 | 0.42 | 0.73 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1123 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1113 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1066 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5L03 · Crystal structure of 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE Synthase from… · 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 A0A069B2G5
- Elsewhere: RCSB PDB 5L03 · PDBe 5L03 · UniProt A0A069B2G5
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