MolNFT v1 · #20684 · protein
Recombinant cyclophilin a from human T cell
1RMH: “Recombinant cyclophilin a from human T cell”. X-ray diffraction, 1 ligand (NIT), 3 pockets (best druggability 0.53). MolNFT v1 #20684 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1RMH
- Type
- protein
- Length
- 336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclophilin a; Aapf peptide substrate
- UniProt
- P05092
- Ligands
- NIT
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclophilin a | protein | 164 | 14% helix, 34% strand | P05092 |
| C, D | Aapf peptide substrate | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- NIT · 4-nitroaniline · ligand · 2 copies · chains A, B, C, D
- SIN · Succinic acid · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.53 | 0.77 | 33 | NIT |
| 2 | 58 | 0.30 | 0.76 | 17 | SIN |
| 3 | 54 | 0.30 | 0.76 | 18 | SIN |
Interfaces
6 interfaces between chains.
- B–D · 267 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 250 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 211 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 58 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct, covalent ligand).
Compared structures
- 1RMH · Recombinant cyclophilin a from human T cell · 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
- Every structure of UniProt P05092
- Elsewhere: RCSB PDB 1RMH · PDBe 1RMH · UniProt P05092
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