Research workbench
Trimeric human arginase 1 in complex with MAB1 - 2 HARG:2 MAB1 complex
Analyse Trimeric human arginase 1 in complex with MAB1 - 2 HARG:2 MAB1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LEZ
- Type
- protein
- Length
- 3,654 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAB1 heavy chain; MAB1 light chain; Arginase-1
- EC
- 3.5.3.1
- UniProt
- P05089
- Ligands
- MN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, G, R, Q | MAB1 heavy chain | protein | 224 | 0% helix, 41% strand | — |
| E, I, P, O | MAB1 light chain | protein | 214 | 7% helix, 32% strand | — |
| A, B, C, M, N, J | Arginase-1 (EC 3.5.3.1) | protein | 317 | 39% helix, 15% strand | P05089 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, M, N, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.86 | 0.87 | 110 | empty |
| 2 | 719 | 0.82 | 0.86 | 71 | empty |
| 3 | 698 | 0.82 | 0.86 | 68 | empty |
| 4 | 391 | 0.78 | 0.87 | 47 | empty |
| 5 | 654 | 0.77 | 0.82 | 83 | empty |
Interfaces
30 interfaces between chains.
- O–Q · 2452 Ų buried · 33 hydrogen bonds · protein-protein
- P–R · 1596 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1569 Ų buried · 8 hydrogen bonds · protein-protein
- I–G · 1468 Ų buried · 11 hydrogen bonds · protein-protein
- M–J · 1293 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7LEZ · Trimeric human Arginase 1 in complex with mAb1 - 2 hArg:2 mAb1 complex · the same entry in another collection · chain Q against Q, 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 P05089
- Elsewhere: RCSB PDB 7LEZ · PDBe 7LEZ · UniProt P05089
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