MolNFT v1 · #156385 · protein
A reaction intermediate of sirohydrochlorin nickelochelatase cfba in complex with NI2+ and sirohydrochlorin
6M2H · Sirohydrochlorin cobaltochelatase: “A reaction intermediate of sirohydrochlorin nickelochelatase cfba in complex with NI2+ and sirohydrochlorin”. X-ray diffraction, 2 ligands (SHN, NI), 1 pocket (best druggability 0.77). MolNFT v1…
- PDB
- 6M2H
- Type
- protein
- Length
- 238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sirohydrochlorin cobaltochelatase
- EC
- 4.99.1.3, 4.99.1.11
- UniProt
- Q58380
- Ligands
- SHN, NI
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sirohydrochlorin cobaltochelatase (EC 4.99.1.3, 4.99.1.11) | protein | 119 | 37% helix, 20% strand | Q58380 |
Ligands and binding sites
- SHN · 3,3',3'',3'''-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic acid · ligand · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.77 | 0.85 | 37 | SHN |
Interfaces
1 interface between chains.
- A–B · 2135 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6M2H · A reaction intermediate of sirohydrochlorin nickelochelatase CfbA in complex with Ni2+… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58380 · AlphaFold monomer V2.0 prediction for sirohydrochlorin cobaltochelatase (Q58380) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q58380
- Elsewhere: RCSB PDB 6M2H · PDBe 6M2H · UniProt Q58380
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