MolNFT v1 · #107700 · protein
Crystal structure of the human rgmb-BMP2 complex, crystal form 2
4UI0 · Bone morphogenetic protein 2: “Crystal structure of the human rgmb-BMP2 complex, crystal form 2”. X-ray diffraction, 1 ligand (CL), 1 pocket (best druggability 0.45). MolNFT v1 #107700 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4UI0
- Type
- protein
- Length
- 261 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bone morphogenetic protein 2; Rgm domain family member B
- UniProt
- P12643, Q6NW40
- Ligands
- CL
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bone morphogenetic protein 2 | protein | 101 | 13% helix, 46% strand | P12643 |
| B | Bone morphogenetic protein 2 | protein | 104 | 16% helix, 44% strand | P12643 |
| C | Rgm domain family member B | protein | 56 | 70% helix, 2% strand | Q6NW40 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.45 | 0.77 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1316 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 473 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 443 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4UI0 · Crystal structure of the human RGMB-BMP2 complex, crystal form 2 · the same entry in another collection · chain A against A, 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 C against A, TM-score 0.96
- P12643 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein 2 (P12643) · a predicted model of the same protein · chain A 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 P12643
- Every structure of UniProt Q6NW40
- Elsewhere: RCSB PDB 4UI0 · PDBe 4UI0 · UniProt P12643 · UniProt Q6NW40
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