MolNFT v1 · #22493 · protein
Nickel superoxide dismutase (nisod) native 1.30 a structure
1T6U · Superoxide dismutase [ni]: “Nickel superoxide dismutase (nisod) native 1.30 a structure”. X-ray diffraction, 1 ligand (NI), 20 pockets (best druggability 0.80). MolNFT v1 #22493 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1T6U
- Type
- protein
- Length
- 1,397 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [ni]
- EC
- 1.15.1.1
- UniProt
- P80735
- Ligands
- NI
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, G, I, J | Superoxide dismutase [ni] (EC 1.15.1.1) | protein | 117 | 79% helix, 0% strand | P80735 |
| D, E, H, K, L | Superoxide dismutase [ni] (EC 1.15.1.1) | protein | 116 | 78% helix, 0% strand | P80735 |
| F | Superoxide dismutase [ni] (EC 1.15.1.1) | protein | 115 | 77% helix, 0% strand | P80735 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 769 | 0.80 | 0.83 | 137 | empty |
| 2 | 328 | 0.74 | 0.86 | 66 | empty |
| 3 | 312 | 0.71 | 0.84 | 54 | empty |
| 4 | 69 | 0.62 | 0.91 | 15 | empty |
| 5 | 78 | 0.59 | 0.89 | 16 | empty |
Interfaces
27 interfaces between chains.
- I–K · 962 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 956 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 955 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 951 Ų buried · 13 hydrogen bonds · protein-protein
- G–J · 938 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1T6U · Nickel Superoxide Dismutase (NiSOD) Native 1.30 A Structure · 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 P80735
- Elsewhere: RCSB PDB 1T6U · PDBe 1T6U · UniProt P80735
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