MolNFT v1 · #29237 · protein
Crystal structure of MDIA1 gbd-FH3 in complex with rhoc-gmppnp
1Z2C · Rho-related GTP-binding protein rhoc: “Crystal structure of MDIA1 gbd-FH3 in complex with rhoc-gmppnp”. X-ray diffraction, 2 ligands (GNP, MG), 13 pockets (best druggability 0.60). MolNFT v1 #29237 on GenesisL1: 3D structure…
- PDB
- 1Z2C
- Type
- protein
- Length
- 1,039 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rho-related GTP-binding protein rhoc; Diaphanous protein homolog 1
- UniProt
- P08134, O08808
- Ligands
- GNP, MG
- Pockets
- 13 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Rho-related GTP-binding protein rhoc | protein | 179 | 37% helix, 26% strand | P08134 |
| B | Diaphanous protein homolog 1 | protein | 346 | 73% helix, 0% strand | O08808 |
| D | Diaphanous protein homolog 1 | protein | 335 | 72% helix, 0% strand | O08808 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.60 | 0.76 | 47 | empty |
| 2 | 294 | 0.58 | 0.77 | 39 | empty |
| 3 | 195 | 0.56 | 0.80 | 36 | MG, GNP |
| 4 | 174 | 0.54 | 0.79 | 35 | MG, GNP |
| 5 | 166 | 0.53 | 0.79 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1336 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1110 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 671 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 188 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 83 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1Z2C · Crystal structure of mDIA1 GBD-FH3 in complex with RhoC-GMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
- P08134 · AlphaFold monomer V2.0 prediction for rho-related GTP-binding protein rhoc (P08134) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O08808 · AlphaFold monomer V2.0 prediction for protein diaphanous homolog 1 (O08808) · a predicted model of the same protein · chain D against A, TM-score 0.82
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 P08134
- Every structure of UniProt O08808
- Elsewhere: RCSB PDB 1Z2C · PDBe 1Z2C · UniProt P08134 · UniProt O08808
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