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Crystal structure of a guanine nucleotide exchange factor (gef) domain from the orientia tsutsugamushi protein otdub
Analyse Crystal structure of a guanine nucleotide exchange factor (gef) domain from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X1H
- Type
- protein
- Length
- 1,279 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ULP_PROTEASE domain-containing protein
- UniProt
- B3CVM3
- Ligands
- NI
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | ULP_PROTEASE domain-containing protein | protein | 215 | 72% helix, 1% strand | B3CVM3 |
| D | ULP_PROTEASE domain-containing protein | protein | 216 | 73% helix, 1% strand | B3CVM3 |
| B, A | ULP_PROTEASE domain-containing protein | protein | 211 | 72% helix, 1% strand | B3CVM3 |
| F, C | ULP_PROTEASE domain-containing protein | protein | 213 | 72% helix, 1% strand | B3CVM3 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.75 | 0.78 | 67 | empty |
| 2 | 587 | 0.72 | 0.80 | 41 | empty |
| 3 | 947 | 0.70 | 0.75 | 97 | empty |
| 4 | 503 | 0.68 | 0.79 | 59 | empty |
| 5 | 580 | 0.64 | 0.75 | 50 | empty |
Interfaces
7 interfaces between chains.
- B–A · 1085 Ų buried · 19 hydrogen bonds · protein-protein
- E–D · 798 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 582 Ų buried · 8 hydrogen bonds · protein-protein
- D–B · 578 Ų buried · 5 hydrogen bonds · protein-protein
- D–C · 568 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6X1H · Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia… · the same entry in another collection · chain E against E, 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 B3CVM3
- Elsewhere: RCSB PDB 6X1H · PDBe 6X1H · UniProt B3CVM3
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