1DNW
HUMAN MYELOPEROXIDASE-CYANIDE-THIOCYANATE COMPLEX
- PDB DOI: https://doi.org/10.2210/pdb1DNW/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Homo sapiens
- Mutation(s): Yes 
- Deposited: 1999-12-16 Released: 2001-12-21 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.224 
- R-Value Work: 0.197 
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
MYELOPEROXIDASE | A, C [auth B] | 104 | Homo sapiens | Mutation(s): 0  EC: 1.11.1.7 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P05164 (Homo sapiens) Explore P05164  Go to UniProtKB:  P05164 | |||||
PHAROS:  P05164 GTEx:  ENSG00000005381  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P05164 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
MYELOPEROXIDASE | B [auth C], D | 466 | Homo sapiens | Mutation(s): 1  EC: 1.11.1.7 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P05164 (Homo sapiens) Explore P05164  Go to UniProtKB:  P05164 | |||||
PHAROS:  P05164 GTEx:  ENSG00000005381  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P05164 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | E, F | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ |
Small Molecules
Ligands 7 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
HEM Query on HEM | P [auth C], X [auth B] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L | |||
NAG Query on NAG | J [auth C], K [auth C], Y [auth D], Z [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | H [auth A], M [auth C], U [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
ACY Query on ACY | CA [auth D] DA [auth D] EA [auth D] Q [auth C] R [auth C] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N | |||
SCN Query on SCN | G [auth A], N [auth C], T [auth B], V [auth B] | THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M | |||
CA Query on CA | AA [auth D], L [auth C] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CYN Query on CYN | BA [auth D], I [auth A], O [auth C], W [auth B] | CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
CSO Query on CSO | B [auth C], D | L-PEPTIDE LINKING | C3 H7 N O3 S | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.224 
- R-Value Work: 0.197 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 111.26 | α = 90 |
b = 63.77 | β = 97.51 |
c = 92.6 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | model building |
X-PLOR | refinement |
X-PLOR | phasing |
Entry History 
Deposition Data
- Released Date: 2001-12-21  Deposition Author(s): Blair-Johnson, M., Fiedler, T.J., Fenna, R.E.
Revision History (Full details and data files)
- Version 1.0: 2001-12-21
Type: Initial release - Version 1.1: 2008-04-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.3: 2018-01-31
Changes: Experimental preparation - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary