Research workbench
Crystal structure of apo mend from M. tuberculosis - P212121
Analyse Crystal structure of apo mend from M. tuberculosis - P212121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ERY
- Type
- protein
- Length
- 1,971 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase
- EC
- 2.2.1.9
- UniProt
- P9WK11
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 504 | 39% helix, 19% strand | P9WK11 |
| D | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 498 | 39% helix, 19% strand | P9WK11 |
| C | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 473 | 38% helix, 20% strand | P9WK11 |
| B | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 496 | 40% helix, 20% strand | P9WK11 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.80 | 0.83 | 70 | empty |
| 2 | 697 | 0.80 | 0.84 | 66 | empty |
| 3 | 254 | 0.67 | 0.84 | 50 | empty |
| 4 | 488 | 0.67 | 0.78 | 60 | empty |
| 5 | 167 | 0.65 | 0.86 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2393 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1531 Ų buried · 41 hydrogen bonds · protein-protein
- D–B · 1518 Ų buried · 36 hydrogen bonds · protein-protein
- C–B · 1498 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 422 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ERY · Crystal Structure of APO MenD from M. tuberculosis - P212121 · the same entry in another collection · chain B against B, TM-score 1.00
- P9WK11 · AlphaFold monomer V2.0 prediction for 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-c… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P9WK11
- Elsewhere: RCSB PDB 5ERY · PDBe 5ERY · UniProt P9WK11
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.