MolNFT v1 · #14208 · protein
Chemical crosslink of nitrogenase mofe protein and fe protein
1M1Y · Nitrogenase molybdenum-iron protein alpha chain: “Chemical crosslink of nitrogenase mofe protein and fe protein”. X-ray diffraction, 5 ligands (HCA, CFM, CLF), 20 pockets (best druggability 0.88). MolNFT v1 #14208 on GenesisL1: 3D…
- PDB
- 1M1Y
- Type
- protein
- Length
- 6,296 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase molybdenum-iron protein alpha chain; Nitrogenase molybdenum-iron protein beta…
- EC
- 1.18.6.1
- UniProt
- P07328, P07329, P00459
- Ligands
- HCA, CFM, CLF, SF4, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, I, K | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 477 | 48% helix, 15% strand | P07328 |
| B, D, J, L | Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1) | protein | 522 | 52% helix, 11% strand | P07329 |
| E, G, M, O | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 286 | 35% helix, 14% strand | P00459 |
| F, H, N, P | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 289 | 40% helix, 16% strand | P00459 |
Ligands and binding sites
- HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 4 copies · chains A, B, C, D, I, J, K, L
- CFM · Fe-Mo-S cluster · ligand · 4 copies · chains A, C, I, K
- CLF · FE(8)-S(7) cluster · ligand · 4 copies · chains A, B, C, D, I, J, K, L
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains E, F, G, H, M, N, O, P
- CA · Calcium ion · metal · 4 copies · chains B, C, D, A, J, K, L, I
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 | 503 | 0.88 | 0.94 | 72 | HCA, CFM |
| 2 | 488 | 0.87 | 0.94 | 66 | HCA, CFM |
| 3 | 457 | 0.87 | 0.95 | 62 | HCA, CFM |
| 4 | 447 | 0.86 | 0.94 | 56 | HCA, CFM |
| 5 | 1103 | 0.85 | 0.86 | 77 | empty |
Interfaces
28 interfaces between chains.
- C–D · 4681 Ų buried · 55 hydrogen bonds · protein-protein
- K–L · 4680 Ų buried · 50 hydrogen bonds · protein-protein
- I–J · 4672 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 4668 Ų buried · 52 hydrogen bonds · protein-protein
- J–L · 3182 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 1M1Y · Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein · the same entry in another collection · chain P against P, 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 P07328
- Every structure of UniProt P07329
- Every structure of UniProt P00459
- Elsewhere: RCSB PDB 1M1Y · PDBe 1M1Y · UniProt P07328 · UniProt P07329 · UniProt P00459
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