MolNFT v1 · #177162 · protein
Crystal structure of POMGNT2 in complex with udp and mono-mannosyl peptide (379MAN short peptide)
7E9L · Protein O-linked-mannose beta-1,4-N…: “Crystal structure of POMGNT2 in complex with udp and mono-mannosyl peptide (379MAN short peptide)”. X-ray diffraction, 5 ligands (UDP, ACE, NAG), 14 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 7E9L
- Type
- protein
- Length
- 1,051 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2; Mono-mannosyl…
- EC
- 2.4.1.312
- UniProt
- Q5NDF2
- Ligands
- UDP, ACE, NAG, MAN, NH2
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2 (EC 2.4.1.312) | protein | 524 | 28% helix, 28% strand | Q5NDF2 |
| B | Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2 (EC 2.4.1.312) | protein | 515 | 28% helix, 27% strand | Q5NDF2 |
| C | Mono-mannosyl peptide (379MAN short peptide) | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- ACE · Acetyl group · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · chains A, C
- NH2 · Amino group · ion · chains B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.74 | 0.83 | 49 | ACE, UDP, TRS, MAN |
| 2 | 742 | 0.74 | 0.79 | 86 | empty |
| 3 | 467 | 0.68 | 0.79 | 46 | UDP |
| 4 | 382 | 0.62 | 0.77 | 40 | empty |
| 5 | 327 | 0.59 | 0.77 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3019 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 460 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 400 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 7 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand, O-glycosylation).
Compared structures
- 7E9L · Crystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man short… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5NDF2 · AlphaFold monomer V2.0 prediction for protein O-linked-mannose… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q5NDF2
- Elsewhere: RCSB PDB 7E9L · PDBe 7E9L · UniProt Q5NDF2
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