Research workbench
Crystal structure of the human rgmc-BMP2 complex
Analyse Crystal structure of the human rgmc-BMP2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UI1
- Type
- protein
- Length
- 353 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bone morphogenetic protein 2; Hemojuvelin
- UniProt
- P12643, Q6ZVN8
- Ligands
- NO3, CL
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bone morphogenetic protein 2 | protein | 104 | 14% helix, 45% strand | P12643 |
| B | Bone morphogenetic protein 2 | protein | 105 | 14% helix, 45% strand | P12643 |
| C | Hemojuvelin | protein | 72 | 67% helix, 0% strand | Q6ZVN8 |
| D | Hemojuvelin | protein | 72 | 71% helix, 0% strand | Q6ZVN8 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 6 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, D, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.59 | 0.78 | 36 | NO3 |
| 2 | 193 | 0.57 | 0.80 | 38 | CL |
| 3 | 126 | 0.44 | 0.77 | 28 | NO3, EDO |
| 4 | 113 | 0.36 | 0.73 | 23 | empty |
| 5 | 97 | 0.33 | 0.73 | 21 | NO3 |
Interfaces
5 interfaces between chains.
- A–B · 1284 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 574 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 525 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 429 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 401 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 4UI1 · Crystal structure of the human RGMC-BMP2 complex · the same entry in another collection · chain D against D, TM-score 1.00
- 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 0.93
- Q6ZVN8 · AlphaFold monomer V2.0 prediction for hemojuvelin (Q6ZVN8) · a predicted model of the same protein · chain C 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 Q6ZVN8
- Elsewhere: RCSB PDB 4UI1 · PDBe 4UI1 · UniProt P12643 · UniProt Q6ZVN8
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