MolNFT v1 · #123932 · protein
Crystal structure of udp-N-acetylenolpyruvoylglucosamine reductase (murb) from mycobacterium tuberculosis
5JZX: “Crystal structure of udp-N-acetylenolpyruvoylglucosamine reductase (murb) from mycobacterium tuberculosis”. X-ray diffraction, 2 ligands (FAD, K), 19 pockets (best druggability 0.84). MolNFT v1 #123932 on GenesisL1: 3D structure…
- PDB
- 5JZX
- Type
- protein
- Length
- 2,051 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylenolpyruvoylglucosamine reductase
- EC
- 1.3.1.98
- UniProt
- P9WJL9
- Ligands
- FAD, K
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) | protein | 364 | 28% helix, 25% strand | P9WJL9 |
| B | Udp-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) | protein | 327 | 27% helix, 26% strand | P9WJL9 |
| C | Udp-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) | protein | 355 | 29% helix, 24% strand | P9WJL9 |
| D | Udp-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) | protein | 353 | 29% helix, 27% strand | P9WJL9 |
| E | Udp-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) | protein | 313 | 27% helix, 25% strand | P9WJL9 |
| F | Udp-N-acetylenolpyruvoylglucosamine reductase (EC 1.3.1.98) | protein | 339 | 27% helix, 22% strand | P9WJL9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.84 | 0.89 | 65 | FAD, K |
| 2 | 901 | 0.84 | 0.85 | 94 | FAD |
| 3 | 598 | 0.83 | 0.88 | 68 | FAD |
| 4 | 1064 | 0.82 | 0.83 | 105 | FAD, K |
| 5 | 912 | 0.81 | 0.83 | 85 | FAD |
Interfaces
4 interfaces between chains.
- B–D · 722 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 711 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 699 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 203 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5JZX · Crystal Structure of UDP-N-acetylenolpyruvoylglucosamine reductase (MurB) from… · the same entry in another collection · chain F against F, TM-score 1.00
- P9WJL9 · AlphaFold monomer V2.0 prediction for udp-N- acetylenolpyruvoylglucosamine reductase… · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P9WJL9
- Elsewhere: RCSB PDB 5JZX · PDBe 5JZX · UniProt P9WJL9
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