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Crystal structure of udp-glcnac 2-epimerase from neisseria meningitidis bound to udp-glcnac
Analyse Crystal structure of udp-glcnac 2-epimerase from neisseria meningitidis bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VLC
- Type
- protein
- Length
- 1,473 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
- A0A0U1RGY0
- Ligands
- UD1
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 371 | 50% helix, 15% strand | A0A0U1RGY0 |
| B | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 366 | 49% helix, 15% strand | A0A0U1RGY0 |
| D | Udp-N-acetylglucosamine 2-epimerase (EC 5.1.3.14) | protein | 365 | 50% helix, 15% strand | A0A0U1RGY0 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.80 | 0.84 | 62 | UD1 |
| 2 | 893 | 0.79 | 0.82 | 67 | UD1 |
| 3 | 1028 | 0.73 | 0.76 | 96 | empty |
| 4 | 400 | 0.71 | 0.82 | 46 | empty |
| 5 | 605 | 0.66 | 0.76 | 61 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1429 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1403 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 910 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6VLC · Crystal structure of UDP-GlcNAc 2-epimerase from Neisseria meningitidis bound to… · 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 A0A0U1RGY0
- Elsewhere: RCSB PDB 6VLC · PDBe 6VLC · UniProt A0A0U1RGY0
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