Research workbench
Crystal structure of human intrinsic factor- cobalamin complex at 2.6 a resolution
Analyse Crystal structure of human intrinsic factor- cobalamin complex at 2.6 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PMV
- Type
- protein
- Length
- 1,290 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gastric intrinsic factor
- UniProt
- P27352
- Ligands
- B12, NAG
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Gastric intrinsic factor | protein | 378 | 48% helix, 13% strand | P27352 |
| B, D | Gastric intrinsic factor | protein | 267 | 61% helix, 1% strand | P27352 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.76 | 0.82 | 63 | empty |
| 2 | 640 | 0.76 | 0.82 | 60 | empty |
| 3 | 1095 | 0.72 | 0.75 | 77 | B12 |
| 4 | 971 | 0.72 | 0.75 | 70 | B12 |
| 5 | 58 | 0.64 | 0.94 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1346 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1279 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 553 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 12 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2PMV · Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P27352 · AlphaFold monomer V2.0 prediction for cobalamin binding intrinsic factor (P27352) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P27352
- Elsewhere: RCSB PDB 2PMV · PDBe 2PMV · UniProt P27352
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