Research workbench
Crystal structure of POMGNT2 in complex with udp and mono-mannosyl peptide (379MAN long peptide)
Analyse Crystal structure of POMGNT2 in complex with udp and mono-mannosyl peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E9K
- Type
- protein
- Length
- 2,136 residues
- Chains
- 6
- 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, NAG, MAN, NH2
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 26% 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 | 527 | 27% helix, 25% strand | Q5NDF2 |
| B | Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2 (EC 2.4.1.312) | protein | 521 | 27% helix, 26% strand | Q5NDF2 |
| D | Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2 (EC 2.4.1.312) | protein | 525 | 28% helix, 26% strand | Q5NDF2 |
| E | Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2 (EC 2.4.1.312) | protein | 524 | 27% helix, 26% strand | Q5NDF2 |
| C | Mono-mannosyl peptide (379MAN long peptide) | protein | 19 | 0% helix, 53% strand | — |
| F | Mono-mannosyl peptide (379MAN long peptide) | protein | 20 | 0% helix, 50% strand | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains D, A, B, E
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, C, D, F
- NH2 · Amino group · ion · 2 copies · chains B, C, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.76 | 0.80 | 84 | empty |
| 2 | 594 | 0.76 | 0.82 | 54 | UDP, TRS, MAN |
| 3 | 527 | 0.75 | 0.83 | 54 | UDP, TRS, MAN |
| 4 | 775 | 0.72 | 0.78 | 70 | empty |
| 5 | 474 | 0.69 | 0.80 | 42 | UDP |
Interfaces
10 interfaces between chains.
- A–B · 2987 Ų buried · 41 hydrogen bonds · protein-protein
- D–E · 2969 Ų buried · 40 hydrogen bonds · protein-protein
- D–F · 660 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 614 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 466 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 16 disulfide (disulfide, N-glycosylation, O-glycosylation, glycosylation).
Compared structures
- 7E9K · Crystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man long… · the same entry in another collection · chain F against F, 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 0.93
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 7E9K · PDBe 7E9K · UniProt Q5NDF2
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