MolNFT v1 · #37242 · protein
Crystal structure analysis of human rcd-1 conserved region
2FV2 · RCD1 required for cell DIFFERENTIATION1 homolog: “Crystal structure analysis of human rcd-1 conserved region”. X-ray diffraction, 1 ligand (MN), 9 pockets (best druggability 0.71). MolNFT v1 #37242 on GenesisL1: 3D structure…
- PDB
- 2FV2
- Type
- protein
- Length
- 1,069 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RCD1 required for cell DIFFERENTIATION1 homolog
- Ligands
- MN
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RCD1 required for cell DIFFERENTIATION1 homolog | protein | 267 | 75% helix, 1% strand | — |
| B | RCD1 required for cell DIFFERENTIATION1 homolog | protein | 266 | 77% helix, 0% strand | — |
| C, D | RCD1 required for cell DIFFERENTIATION1 homolog | protein | 268 | 71% helix, 0% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.71 | 0.75 | 80 | empty |
| 2 | 628 | 0.62 | 0.74 | 45 | empty |
| 3 | 204 | 0.60 | 0.81 | 35 | empty |
| 4 | 250 | 0.57 | 0.78 | 38 | empty |
| 5 | 248 | 0.54 | 0.77 | 29 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1030 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 994 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 332 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 73 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2FV2 · Crystal Structure Analysis of human Rcd-1 conserved region · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 2FV2 · PDBe 2FV2
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