MolNFT v1 · #53415 · protein
Mure ligase of mycobacterium tuberculosis
2WTZ · Udp-N-acetylmuramoyl-L-alanyl-D-glutamate…: “Mure ligase of mycobacterium tuberculosis”. X-ray diffraction, 2 ligands (UAG, MG), 20 pockets (best druggability 0.80). MolNFT v1 #53415 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2WTZ
- Type
- protein
- Length
- 1,919 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramoyl-L-alanyl-D-glutamate- -2,6-diaminopimelate ligase
- EC
- 6.3.2.13
- UniProt
- P65477
- Ligands
- UAG, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramoyl-L-alanyl-D-glutamate- -2,6-diaminopimelate ligase (EC 6.3.2.13) | protein | 504 | 34% helix, 21% strand | P65477 |
| B | Udp-N-acetylmuramoyl-L-alanyl-D-glutamate- -2,6-diaminopimelate ligase (EC 6.3.2.13) | protein | 508 | 35% helix, 21% strand | P65477 |
| C | Udp-N-acetylmuramoyl-L-alanyl-D-glutamate- -2,6-diaminopimelate ligase (EC 6.3.2.13) | protein | 439 | 35% helix, 23% strand | P65477 |
| D | Udp-N-acetylmuramoyl-L-alanyl-D-glutamate- -2,6-diaminopimelate ligase (EC 6.3.2.13) | protein | 468 | 35% helix, 21% strand | P65477 |
Ligands and binding sites
- UAG · Uridine-5'-diphosphate-N-acetylmuramoyl-L-alanine-D-glutamate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.80 | 0.82 | 81 | empty |
| 2 | 988 | 0.79 | 0.81 | 80 | empty |
| 3 | 1054 | 0.79 | 0.81 | 97 | empty |
| 4 | 524 | 0.71 | 0.80 | 55 | MG |
| 5 | 593 | 0.70 | 0.79 | 64 | MG |
Interfaces
3 interfaces between chains.
- A–B · 1263 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 848 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 817 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 2WTZ · MurE ligase of Mycobacterium Tuberculosis · 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 P65477
- Elsewhere: RCSB PDB 2WTZ · PDBe 2WTZ · UniProt P65477
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