Research workbench
Anaerobic cobalt chelatase from archeaoglobus fulgidus ( cbix) in complex with metalated sirohydrochlorin product
Analyse Anaerobic cobalt chelatase from archeaoglobus fulgidus ( cbix) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XWQ
- Type
- protein
- Length
- 502 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sirohydrochlorin cobaltochelatase
- EC
- 4.99.1.3
- UniProt
- O29537
- Ligands
- SIR
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Sirohydrochlorin cobaltochelatase (EC 4.99.1.3) | protein | 126 | 35% helix, 23% strand | O29537 |
| B, D | Sirohydrochlorin cobaltochelatase (EC 4.99.1.3) | protein | 125 | 37% helix, 23% strand | O29537 |
Ligands and binding sites
- SIR · Cobalt sirohydrochlorin · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.71 | 0.85 | 31 | SIR |
| 2 | 272 | 0.71 | 0.85 | 30 | SIR |
| 3 | 216 | 0.59 | 0.81 | 38 | empty |
| 4 | 85 | 0.45 | 0.81 | 17 | empty |
| 5 | 80 | 0.43 | 0.80 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2307 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2235 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 671 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 615 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 436 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2XWQ · Anaerobic cobalt chelatase from Archeaoglobus fulgidus (CbiX) in complex with metalated… · the same entry in another collection · chain D against D, TM-score 1.00
- O29537 · AlphaFold monomer V2.0 prediction for sirohydrochlorin cobaltochelatase (O29537) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 O29537
- Elsewhere: RCSB PDB 2XWQ · PDBe 2XWQ · UniProt O29537
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