Research workbench
Crystal structure of mgadp bound AV2-AV1 complex
Analyse Crystal structure of mgadp bound AV2-AV1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AFI
- Type
- protein
- Length
- 6,137 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase molybdenum-iron protein; Nitrogenase iron protein 1
- EC
- 1.18.6.1
- UniProt
- P07328, P07329, P00459
- Ligands
- ADP, HCA, CFN, CLF, SF4, MG, CA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 10 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, I, K | Nitrogenase molybdenum-iron protein (EC 1.18.6.1) | protein | 476 | 49% helix, 15% strand | P07328 |
| B, D, J, L | Nitrogenase molybdenum-iron protein (EC 1.18.6.1) | protein | 522 | 53% helix, 11% strand | P07329 |
| E | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 271 | 42% helix, 16% strand | P00459 |
| F | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 275 | 42% helix, 16% strand | P00459 |
| G | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 263 | 40% helix, 16% strand | P00459 |
| H | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 269 | 43% helix, 16% strand | P00459 |
| M | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 268 | 44% helix, 16% strand | P00459 |
| N | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 270 | 43% helix, 16% strand | P00459 |
| O | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 262 | 40% helix, 15% strand | P00459 |
| P | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 267 | 44% helix, 15% strand | P00459 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains E, F, G, H, M, N, O, P
- HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 4 copies · chains A, B, C, D, I, J, K, L
- CFN · FE(7)-Mo-S(9)-N 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
- MG · Magnesium ion · metal · 8 copies · chains E, F, G, H, M, N, O, P
- CA · Calcium ion · metal · 4 copies · chains A, B, D, C, 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 | 594 | 0.89 | 0.95 | 75 | HCA, CFN |
| 2 | 602 | 0.89 | 0.94 | 72 | HCA, CFN |
| 3 | 603 | 0.88 | 0.94 | 78 | HCA, CFN |
| 4 | 601 | 0.88 | 0.94 | 77 | HCA, CFN |
| 5 | 983 | 0.86 | 0.87 | 104 | MG, ADP |
Interfaces
33 interfaces between chains.
- C–D · 4638 Ų buried · 59 hydrogen bonds · protein-protein
- K–L · 4635 Ų buried · 59 hydrogen bonds · protein-protein
- I–J · 4621 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 4606 Ų buried · 55 hydrogen bonds · protein-protein
- B–D · 3027 Ų buried · 67 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2AFI · Crystal Structure of MgADP bound Av2-Av1 Complex · the same entry in another collection · chain K against K, 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 2AFI · PDBe 2AFI · UniProt P07328 · UniProt P07329 · UniProt P00459
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