MolNFT v1 · #107702 · protein
Crystal structure of the ternary rgmb-BMP2-NEO1 complex
4UI2 · Neogenin: “Crystal structure of the ternary rgmb-BMP2-NEO1 complex”. X-ray diffraction, 3 ligands (SRT, NAG, BMA), 4 pockets (best druggability 0.67). MolNFT v1 #107702 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UI2
- Type
- protein
- Length
- 541 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neogenin; Bone morphogenetic protein 2, BMP2; Repulsive guidance molecule C, rgmc…
- UniProt
- P97798, P12643, Q6NW40
- Ligands
- SRT, NAG, BMA
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neogenin | protein | 201 | 1% helix, 49% strand | P97798 |
| B | Bone morphogenetic protein 2, BMP2 | protein | 104 | 19% helix, 42% strand | P12643 |
| C | Repulsive guidance molecule C, rgmc, hemojuvelin | protein | 80 | 55% helix, 9% strand | Q6NW40 |
| D | Repulsive guidance molecule C, rgmc, hemojuvelin | protein | 156 | 9% helix, 47% strand | Q6NW40 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · 3 copies · chains B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.67 | 0.84 | 37 | empty |
| 2 | 150 | 0.45 | 0.76 | 27 | empty |
| 3 | 148 | 0.43 | 0.75 | 23 | empty |
| 4 | 75 | 0.37 | 0.77 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1183 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1089 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 470 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 425 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 4UI2 · Crystal structure of the ternary RGMB-BMP2-NEO1 complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q6NW40 · AlphaFold monomer V2.0 prediction for rgm domain family member B (Q6NW40) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P12643 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein 2 (P12643) · a predicted model of the same protein · chain B against A, TM-score 0.91
- P97798 · AlphaFold monomer V2.0 prediction for neogenin (P97798) · a predicted model of the same protein · chain A against A, TM-score 0.75
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 P97798
- Every structure of UniProt P12643
- Every structure of UniProt Q6NW40
- Elsewhere: RCSB PDB 4UI2 · PDBe 4UI2 · UniProt P97798 · UniProt P12643 · UniProt Q6NW40
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