MolNFT v1 · #118108 · protein
Re-refinement of integrin ALPHAXBETA2 ectodomain in the CLOSED/BENT conformation
5ES4 · Integrin alpha-X: “Re-refinement of integrin ALPHAXBETA2 ectodomain in the CLOSED/BENT conformation”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.84). MolNFT v1 #118108 on GenesisL1: 3D structure…
- PDB
- 5ES4
- Type
- protein
- Length
- 6,427 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-X; Integrin beta-2
- UniProt
- P20702, P05107
- Ligands
- NAG, MAN, BMA, CA, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-X | protein | 1080 | 11% helix, 44% strand | P20702 |
| B, D, F, H | Integrin beta-2 | protein | 674 | 17% helix, 27% strand | P05107 |
| C, E | Integrin alpha-X | protein | 884 | 4% helix, 47% strand | P20702 |
| G | Integrin alpha-X | protein | 883 | 5% helix, 46% strand | P20702 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 61 copies · chains A, B, C, D, E, F, G, H
- MAN · alpha-D-mannopyranose · sugar · 35 copies · chains A, C, F, E, G
- BMA · beta-D-mannopyranose · sugar · 16 copies · chains A, E, G
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · chains A
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 | 1157 | 0.84 | 0.85 | 108 | empty |
| 2 | 1052 | 0.84 | 0.85 | 95 | empty |
| 3 | 916 | 0.84 | 0.85 | 86 | empty |
| 4 | 994 | 0.82 | 0.83 | 88 | empty |
| 5 | 559 | 0.80 | 0.87 | 83 | empty |
Interfaces
10 interfaces between chains.
- A–B · 3517 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 3391 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 3292 Ų buried · 40 hydrogen bonds · protein-protein
- G–H · 3119 Ų buried · 26 hydrogen bonds · protein-protein
- E–G · 2538 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 146 disulfide, 44 glycan (disulfide, N-glycosylation).
Compared structures
- 5ES4 · Re-refinement of integrin ALPHAXBETA2 ectodomain in the CLOSED/BENT conformation · the same entry in another collection · chain H against H, TM-score 1.00
- P05107 · AlphaFold monomer V2.0 prediction for integrin beta-2 (P05107) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P20702 · AlphaFold monomer V2.0 prediction for integrin alpha-X (P20702) · a predicted model of the same protein · chain G against A, TM-score 0.91
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 P20702
- Every structure of UniProt P05107
- Elsewhere: RCSB PDB 5ES4 · PDBe 5ES4 · UniProt P20702 · UniProt P05107
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