MolNFT v1 · #169620 · protein
Apo form of POMGNT2
6XI2 · Protein O-linked-mannose beta-1,4-N…: “Apo form of POMGNT2”. X-ray diffraction, 2 ligands (NAG, PO4), 20 pockets (best druggability 0.71). MolNFT v1 #169620 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XI2
- Type
- protein
- Length
- 2,106 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…
- EC
- 2.4.1.312
- UniProt
- Q8NAT1
- Ligands
- NAG, PO4
- Pockets
- 20 · best druggability 0.71
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 | 528 | 26% helix, 27% strand | Q8NAT1 |
| B | Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2 (EC 2.4.1.312) | protein | 518 | 27% helix, 27% strand | Q8NAT1 |
| D | Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2 (EC 2.4.1.312) | protein | 521 | 27% helix, 26% strand | Q8NAT1 |
| C | Protein O-linked-mannose beta-1,4-N- acetylglucosaminyltransferase 2 (EC 2.4.1.312) | protein | 519 | 28% helix, 26% strand | Q8NAT1 |
| G | Ala-ala-ala-ala-ala-ala-ala-ala-ala-ala | protein | 10 | 0% helix, 20% strand | — |
| H | Ala-gly-ala-gly-ala-ala-ala-ala-ala-ala | protein | 10 | 0% helix, 10% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, D
- PO4 · Phosphate ion · ion · 25 copies · chains A, G, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.71 | 0.80 | 45 | PO4 |
| 2 | 522 | 0.70 | 0.80 | 51 | PO4 |
| 3 | 435 | 0.70 | 0.81 | 40 | PO4 |
| 4 | 449 | 0.68 | 0.80 | 41 | PO4 |
| 5 | 264 | 0.65 | 0.82 | 47 | PO4 |
Interfaces
8 interfaces between chains.
- A–B · 3036 Ų buried · 46 hydrogen bonds · protein-protein
- D–C · 3007 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 588 Ų buried · 5 hydrogen bonds · protein-protein
- D–G · 371 Ų buried · 2 hydrogen bonds · protein-protein
- A–H · 279 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
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 Q8NAT1
- Elsewhere: RCSB PDB 6XI2 · PDBe 6XI2 · UniProt Q8NAT1
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