MolNFT v1 · #177161 · protein
Crystal structure of POMGNT2 in complex with udp and mono-mannosyl peptide (379MAN long peptide)
7E9K: “Crystal structure of POMGNT2 in complex with udp and mono-mannosyl peptide (379MAN long peptide)”. X-ray diffraction, 4 ligands (UDP, NAG, MAN). MolNFT v1 #177161 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E9K
- Type
- protein
- Length
- 2,136 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- Q5NDF2
- Ligands
- UDP, NAG, MAN, NH2
Structure
x-ray diffraction · 6 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 527 | — | Q5NDF2 |
| B | — | protein | 521 | — | Q5NDF2 |
| D | — | protein | 525 | — | Q5NDF2 |
| E | — | protein | 524 | — | Q5NDF2 |
| C | — | protein | 19 | — | — |
| F | — | protein | 20 | — | — |
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.
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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