MolNFT v1 · #92867 · protein
Crystal structure of the SH3 domain of dnmbp protein [homo sapiens]
4GLM · Dynamin-binding protein: “Crystal structure of the SH3 domain of dnmbp protein [homo sapiens]”. X-ray diffraction, 1 ligand (UNX), 1 pocket (best druggability 0.71). MolNFT v1 #92867 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4GLM
- Type
- protein
- Length
- 228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynamin-binding protein
- UniProt
- Q6XZF7
- Ligands
- UNX
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynamin-binding protein | protein | 58 | 5% helix, 52% strand | Q6XZF7 |
| B, D | Dynamin-binding protein | protein | 57 | 5% helix, 53% strand | Q6XZF7 |
| C | Dynamin-binding protein | protein | 56 | 5% helix, 54% strand | Q6XZF7 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 18 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.71 | 0.80 | 59 | empty |
Interfaces
5 interfaces between chains.
- B–C · 440 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 272 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 261 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 205 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 65 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4GLM · Crystal structure of the SH3 Domain of DNMBP protein [Homo sapiens] · the same entry in another collection · chain A against A, TM-score 1.00
- Q6XZF7 · AlphaFold monomer V2.0 prediction for dynamin-binding protein (Q6XZF7) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q6XZF7
- Elsewhere: RCSB PDB 4GLM · PDBe 4GLM · UniProt Q6XZF7
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