Research workbench
Repulsive guidance molecule B (rgmb) in complex with growth differentiation factor 5 (GDF5) (crystal form 1)
Analyse Repulsive guidance molecule B (rgmb) in complex with growth differentiation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z3J
- Type
- protein
- Length
- 362 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GROWTH/DIFFERENTIATION factor 5; Rgm domain family member B
- UniProt
- P43026, Q6NW40
- Ligands
- NAG, CL, SO4
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GROWTH/DIFFERENTIATION factor 5 | protein | 105 | 17% helix, 45% strand | P43026 |
| B | GROWTH/DIFFERENTIATION factor 5 | protein | 106 | 17% helix, 44% strand | P43026 |
| C | Rgm domain family member B | protein | 75 | 67% helix, 0% strand | Q6NW40 |
| D | Rgm domain family member B | protein | 76 | 59% helix, 0% strand | Q6NW40 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains D
- CL · Chloride ion · ion · 3 copies · chains B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, A, D
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.68 | 0.78 | 71 | GOL, EDO |
| 2 | 51 | 0.63 | 0.94 | 17 | EDO |
| 3 | 89 | 0.50 | 0.83 | 29 | EDO |
| 4 | 51 | 0.34 | 0.78 | 13 | SO4 |
| 5 | 51 | 0.27 | 0.74 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1185 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 686 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 672 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 441 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 404 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6Z3J · Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5… · the same entry in another collection · chain D against D, TM-score 1.00
- P43026 · AlphaFold monomer V2.0 prediction for GROWTH/DIFFERENTIATION factor 5 (P43026) · a predicted model of the same protein · chain A against A, TM-score 0.96
- 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 0.96
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 P43026
- Every structure of UniProt Q6NW40
- Elsewhere: RCSB PDB 6Z3J · PDBe 6Z3J · UniProt P43026 · UniProt Q6NW40
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