Research workbench
2.2 ångström resolution crystal structure of putative udp-N- acetylglucosamine 2-epimerase from listeria monocytogenes
Analyse 2.2 ångström resolution crystal structure of putative udp-N- acetylglucosamine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OT5
- Type
- protein
- Length
- 1,497 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine 2-epimerase
- EC
- 5.1.3.14
- UniProt
- Q8Y4B4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 372 | 48% helix, 16% strand | Q8Y4B4 |
| B | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 378 | 47% helix, 16% strand | Q8Y4B4 |
| C | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 376 | 48% helix, 17% strand | Q8Y4B4 |
| D | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 371 | 48% helix, 16% strand | Q8Y4B4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.78 | 0.81 | 70 | empty |
| 2 | 791 | 0.76 | 0.80 | 56 | empty |
| 3 | 1185 | 0.71 | 0.75 | 111 | empty |
| 4 | 524 | 0.65 | 0.76 | 53 | empty |
| 5 | 174 | 0.45 | 0.75 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 348 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 251 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 97 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3OT5 · 2.2 Angstrom Resolution Crystal Structure of putative UDP-N-acetylglucosamine 2-epimerase… · 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 Q8Y4B4
- Elsewhere: RCSB PDB 3OT5 · PDBe 3OT5 · UniProt Q8Y4B4
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