Research workbench
2.05 ångström structure of a divalent-cation tolerance protein (cuta) from yersinia pestis
Analyse 2.05 ångström structure of a divalent-cation tolerance protein (cuta) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GSD
- Type
- protein
- Length
- 1,258 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Divalent-cation tolerance protein cuta
- UniProt
- Q74XD3
- Ligands
- NA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, G, H, I, J, K, L | Divalent-cation tolerance protein cuta | protein | 105 | 34% helix, 41% strand | Q74XD3 |
| D, E | Divalent-cation tolerance protein cuta | protein | 104 | 35% helix, 41% strand | Q74XD3 |
Ligands and binding sites
- NA · Sodium ion · metal · 22 copies · chains A, B, C, I, J, E, D, F, G, H, K, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 13 copies · chains A, C, B, D, F, E, G, I, H, J, L, K
- PEG · Di(hydroxyethyl)ether · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.76 | 0.98 | 18 | empty |
| 2 | 64 | 0.76 | 0.99 | 18 | empty |
| 3 | 57 | 0.75 | 0.99 | 18 | empty |
| 4 | 58 | 0.75 | 0.98 | 18 | empty |
| 5 | 1023 | 0.71 | 0.75 | 79 | NA, EPE |
Interfaces
23 interfaces between chains.
- J–L · 1210 Ų buried · 16 hydrogen bonds · protein-protein
- H–I · 1197 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1191 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1183 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1173 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3GSD · 2.05 Angstrom structure of a divalent-cation tolerance protein (CutA) from Yersinia pestis · 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 Q74XD3
- Elsewhere: RCSB PDB 3GSD · PDBe 3GSD · UniProt Q74XD3
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