Research workbench
Crystal structure of TGFB2 in complex with GC2008.
Analyse Crystal structure of TGFB2 in complex with GC2008. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KXZ
- Type
- protein
- Length
- 2,179 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transforming growth factor beta-2; GC1008 heavy chain; GC1008 light chain
- UniProt
- P61812
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Transforming growth factor beta-2 | protein | 112 | 21% helix, 42% strand | P61812 |
| H, N | GC1008 heavy chain | protein | 223 | 7% helix, 52% strand | — |
| J | GC1008 heavy chain | protein | 217 | 7% helix, 52% strand | — |
| Q | GC1008 heavy chain | protein | 217 | 9% helix, 52% strand | — |
| I | GC1008 light chain | protein | 212 | 6% helix, 51% strand | — |
| L, M, P | GC1008 light chain | protein | 213 | 6% helix, 51% strand | — |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 5 copies · chains A, N, E, H, J, Q, M
- PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · chains D, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.82 | 0.84 | 156 | empty |
| 2 | 439 | 0.73 | 0.83 | 68 | empty |
| 3 | 550 | 0.60 | 0.74 | 69 | empty |
| 4 | 526 | 0.60 | 0.74 | 54 | MES |
| 5 | 378 | 0.57 | 0.75 | 50 | empty |
Interfaces
26 interfaces between chains.
- H–L · 1899 Ų buried · 19 hydrogen bonds · protein-protein
- N–M · 1862 Ų buried · 17 hydrogen bonds · protein-protein
- J–I · 1766 Ų buried · 15 hydrogen bonds · protein-protein
- Q–P · 1754 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1349 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide (disulfide).
Compared structures
- 4KXZ · crystal structure of tgfb2 in complex with GC2008. · the same entry in another collection · chain P against P, 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 P61812
- Elsewhere: RCSB PDB 4KXZ · PDBe 4KXZ · UniProt P61812
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