Research workbench
Trimeric human arginase 1 in complex with MAB3
Analyse Trimeric human arginase 1 in complex with MAB3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LF1
- Type
- protein
- Length
- 4,548 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginase-1; MAB3 heavy chain; MAB3 light chain
- EC
- 3.5.3.1
- UniProt
- P05089
- Ligands
- MN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 18% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, J, M, N | Arginase-1 (EC 3.5.3.1) | protein | 317 | 38% helix, 16% strand | P05089 |
| D, F, G, K, O, P | MAB3 heavy chain | protein | 227 | 1% helix, 32% strand | — |
| E, H, I, L, Q, R | MAB3 light chain | protein | 214 | 6% helix, 37% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, J, M, N
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 | 1029 | 0.87 | 0.89 | 111 | empty |
| 2 | 641 | 0.85 | 0.89 | 72 | empty |
| 3 | 882 | 0.85 | 0.87 | 76 | empty |
| 4 | 783 | 0.85 | 0.87 | 76 | empty |
| 5 | 822 | 0.84 | 0.87 | 76 | empty |
Interfaces
42 interfaces between chains.
- K–L · 2047 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 2045 Ų buried · 20 hydrogen bonds · protein-protein
- O–Q · 1987 Ų buried · 15 hydrogen bonds · protein-protein
- F–H · 1983 Ų buried · 15 hydrogen bonds · protein-protein
- G–I · 1935 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 7LF1 · Trimeric human Arginase 1 in complex with mAb3 · the same entry in another collection · chain N against N, 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 7LF1 · PDBe 7LF1 · UniProt P05089
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