1WVP

Structure of chemically modified myoglobin with distal N-tetrazolyl-histidine E7(64)

PDB DOI: https://doi.org/10.2210/pdb1WVP/pdb

Classification: OXYGEN STORAGE/TRANSPORT
Organism(s): Physeter catodon
Mutation(s): Yes

Deposited: 2004-12-23 Released: 2005-01-18
Deposition Author(s): Makino, M., Sugimoto, H., Kamiya, N., Shiro, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.208
R-Value Work: 0.174
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Heme environmental structure of a novel artificial myoglobin with a closed heme pocket: site-specific chemical modification producing distal N-tetrazolylhistidine E7 by cyanogen bromide and azide ion

Kamiya, N., Shiro, Y., Iwata, T., Iizuka, T., Iwasaki, H.

(1991) J Am Chem Soc 113: 1826-1829

Macromolecule Content

Total Structure Weight: 18.09 kDa
Atom Count: 1,461
Modelled Residue Count: 151
Deposited Residue Count: 153
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	153	Physeter catodon	Mutation(s): 1
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185 Go to UniProtKB: P02185
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02185
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NZH Query on NZH	A	L-PEPTIDE LINKING	C₇ H₉ N₇ O		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.208
R-Value Work: 0.174
R-Value Observed: 0.175
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.982	α = 90
b = 60.982	β = 90
c = 84.808	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-01-18

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2005-01-18
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description

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1WVP

Structure of chemically modified myoglobin with distal N-tetrazolyl-histidine E7(64)

Heme environmental structure of a novel artificial myoglobin with a closed heme pocket: site-specific chemical modification producing distal N-tetrazolylhistidine E7 by cyanogen bromide and azide ion

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)