MolNFT v1 · #38581 · protein
Crystal structure of clc-EC1 in complex with Fab fragment in secn-
2H2P · Clc cl transporter: “Crystal structure of clc-EC1 in complex with Fab fragment in secn-”. X-ray diffraction, 1 ligand (SEK), 18 pockets (best druggability 0.82). MolNFT v1 #38581 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2H2P
- Type
- protein
- Length
- 1,749 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clc cl transporter; Fab fragment, heavy chain; Fab fragment, light chain
- UniProt
- P37019
- Ligands
- SEK
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clc cl transporter | protein | 444 | 73% helix, 0% strand | P37019 |
| B | Clc cl transporter | protein | 441 | 74% helix, 0% strand | P37019 |
| C, E | Fab fragment, heavy chain | protein | 221 | 3% helix, 49% strand | — |
| D, F | Fab fragment, light chain | protein | 211 | 4% helix, 41% strand | — |
Ligands and binding sites
- SEK · Selenocyanate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.82 | 0.87 | 58 | empty |
| 2 | 594 | 0.74 | 0.81 | 62 | empty |
| 3 | 623 | 0.73 | 0.80 | 58 | empty |
| 4 | 343 | 0.66 | 0.80 | 31 | SEK |
| 5 | 304 | 0.63 | 0.80 | 29 | SEK |
Interfaces
11 interfaces between chains.
- A–B · 3495 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1992 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1948 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 469 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 448 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2H2P · Crystal structure of CLC-ec1 in complex with Fab fragment in SeCN- · the same entry in another collection · chain F against F, TM-score 1.00
- P37019 · AlphaFold monomer V2.0 prediction for H(+)/CL(-) exchange transporter clca (P37019) · a predicted model of the same protein · chain B 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 P37019
- Elsewhere: RCSB PDB 2H2P · PDBe 2H2P · UniProt P37019
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