MolNFT v1 · #66550 · protein
Crystal structure of MMS21 and SMC5 complex
3HTK · Structural maintenance of chromosomes protein 5: “Crystal structure of MMS21 and SMC5 complex”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.54). MolNFT v1 #66550 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3HTK
- Type
- protein
- Length
- 387 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural maintenance of chromosomes protein 5; E3 sumo-protein ligase MMS21
- EC
- 6.3.2.-
- UniProt
- Q08204, P38632
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural maintenance of chromosomes protein 5 | protein | 60 | 90% helix, 0% strand | Q08204 |
| B | Structural maintenance of chromosomes protein 5 | protein | 73 | 90% helix, 0% strand | Q08204 |
| C | E3 sumo-protein ligase MMS21 (EC 6.3.2.-) | protein | 254 | 50% helix, 7% strand | P38632 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.54 | 0.76 | 29 | empty |
| 2 | 201 | 0.52 | 0.77 | 33 | empty |
| 3 | 223 | 0.51 | 0.76 | 21 | empty |
| 4 | 80 | 0.44 | 0.80 | 21 | empty |
| 5 | 109 | 0.41 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2060 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1618 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 673 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3HTK · Crystal structure of Mms21 and Smc5 complex · the same entry in another collection · chain A against A, TM-score 1.00
- P38632 · AlphaFold monomer V2.0 prediction for E3 sumo-protein ligase MMS21 (P38632) · a predicted model of the same protein · chain C against A, TM-score 0.93
- Q08204 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 5… · a predicted model of the same protein · chain B against A, TM-score 0.83
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 Q08204
- Every structure of UniProt P38632
- Elsewhere: RCSB PDB 3HTK · PDBe 3HTK · UniProt Q08204 · UniProt P38632
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