Research workbench
Repulsive guidance molecule B (rgmb) in complex with growth differentiation factor 5 (GDF5) and neogenin 1 (NEO1)
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
- 6Z3M
- Type
- protein
- Length
- 3,257 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GROWTH/DIFFERENTIATION factor 5; Rgm domain family member B; Neogenin
- UniProt
- P43026, Q6NW40, P97798
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 12 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, M | GROWTH/DIFFERENTIATION factor 5 | protein | 105 | 17% helix, 45% strand | P43026 |
| B, G, N | GROWTH/DIFFERENTIATION factor 5 | protein | 106 | 17% helix, 44% strand | P43026 |
| C | Rgm domain family member B | protein | 74 | 68% helix, 0% strand | Q6NW40 |
| D | Rgm domain family member B | protein | 75 | 60% helix, 0% strand | Q6NW40 |
| E, F, K, Q, R | Neogenin | protein | 205 | 1% helix, 49% strand | P97798 |
| I | Rgm domain family member B | protein | 71 | 63% helix, 0% strand | Q6NW40 |
| J | Rgm domain family member B | protein | 73 | 68% helix, 0% strand | Q6NW40 |
| L | Neogenin | protein | 187 | 0% helix, 50% strand | P97798 |
| O | Rgm domain family member B | protein | 71 | 70% helix, 0% strand | Q6NW40 |
| P | Rgm domain family member B | protein | 76 | 59% helix, 0% strand | Q6NW40 |
| c, d, i, j, o, p | Rgm domain family member B | protein | 158 | 9% helix, 47% strand | Q6NW40 |
| S, T, U, V, W, X | Rgm domain family member B | protein | 4 | 0% helix, 0% strand | Q6NW40 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains D, E, F, I, K, L, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.68 | 0.78 | 74 | empty |
| 2 | 492 | 0.68 | 0.79 | 61 | empty |
| 3 | 191 | 0.66 | 0.85 | 33 | empty |
| 4 | 423 | 0.66 | 0.79 | 59 | empty |
| 5 | 194 | 0.64 | 0.84 | 33 | empty |
Interfaces
34 interfaces between chains.
- R–p · 1233 Ų buried · 18 hydrogen bonds · protein-protein
- F–d · 1232 Ų buried · 18 hydrogen bonds · protein-protein
- L–j · 1232 Ų buried · 18 hydrogen bonds · protein-protein
- Q–o · 1231 Ų buried · 18 hydrogen bonds · protein-protein
- E–c · 1231 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6Z3M · Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5… · the same entry in another collection · chain K against K, TM-score 1.00
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
- Every structure of UniProt P97798
- Elsewhere: RCSB PDB 6Z3M · PDBe 6Z3M · UniProt P43026 · UniProt Q6NW40 · UniProt P97798
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.