MolNFT v1 · #152461 · protein + DNA
Human exog-H140A in complex with RNA-DNA chimeric duplex
6IID · Nuclease exog, mitochondrial: “Human exog-H140A in complex with RNA-DNA chimeric duplex”. X-ray diffraction, 1 ligand (MG), 17 pockets (best druggability 0.85). MolNFT v1 #152461 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6IID
- Type
- protein + DNA
- Length
- 1,230 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease exog, mitochondrial; DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)…
- EC
- 3.1.30.-
- UniProt
- Q9Y2C4
- Ligands
- MG
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 12 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 296 | 34% helix, 25% strand | Q9Y2C4 |
| B | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 290 | 31% helix, 26% strand | Q9Y2C4 |
| C | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 291 | 31% helix, 26% strand | Q9Y2C4 |
| D | Nuclease exog, mitochondrial (EC 3.1.30.-) | protein | 288 | 32% helix, 26% strand | Q9Y2C4 |
| E | DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)- R(P*CP*AP*CP*G)-3') | dna | 10 | — | — |
| F | DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3') | dna | 11 | — | — |
| G | DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)- R(P*CP*AP*CP*G)-3') | dna | 7 | — | — |
| H | DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3') | dna | 8 | — | — |
| I | DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)- R(P*CP*AP*CP*G)-3') | dna | 11 | — | — |
| J | DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3') | dna | 9 | — | — |
| K | DNA/RNA (5'-R(P*CP*GP*GP*GP*A)-D(P*T)-R(P*G)-D(P*T)- R(P*CP*AP*CP*G)-3') | dna | 5 | — | — |
| L | DNA (5'-D(*CP*GP*TP*GP*AP*CP*AP*TP*CP*CP*CP*G)-3') | dna | 4 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains B, G, C, I, A, E, D, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.85 | 0.93 | 61 | empty |
| 2 | 1195 | 0.79 | 0.81 | 114 | empty |
| 3 | 938 | 0.77 | 0.80 | 63 | empty |
| 4 | 582 | 0.70 | 0.79 | 37 | empty |
| 5 | 516 | 0.63 | 0.76 | 54 | empty |
Interfaces
17 interfaces between chains.
- A–B · 2739 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2650 Ų buried · 31 hydrogen bonds · protein-protein
- D–K · 693 Ų buried · 32 hydrogen bonds · protein-nucleic
- C–I · 690 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–E · 673 Ų buried · 28 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6IID · Human EXOG-H140A in complex with RNA-DNA chimeric duplex · the same entry in another collection · chain L against L, 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 Q9Y2C4
- Elsewhere: RCSB PDB 6IID · PDBe 6IID · UniProt Q9Y2C4
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