3WCT

The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: Oxygenated form

PDB DOI: https://doi.org/10.2210/pdb3WCT/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Lamellibrachia satsuma
Mutation(s): No

Deposited: 2013-06-01 Released: 2014-06-04
Deposition Author(s): Numoto, N., Nakagawa, T., Ohara, R., Hasegawa, T., Kita, A., Yoshida, T., Maruyama, T., Imai, K., Fukumori, Y., Miki, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.264
R-Value Work: 0.216
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 137.52 kDa
Atom Count: 9,764
Modelled Residue Count: 1,174
Deposited Residue Count: 1,178
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A1 globin chain of giant V2 hemoglobin	A, E	146	Lamellibrachia satsuma	Mutation(s): 0
UniProt
Find proteins for S0BBU7 (Lamellibrachia satsuma) Explore S0BBU7 Go to UniProtKB: S0BBU7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S0BBU7
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
A2 globin chain of giant V2 hemoglobin	B, F	144	Lamellibrachia satsuma	Mutation(s): 0
UniProt
Find proteins for S0BBR6 (Lamellibrachia satsuma) Explore S0BBR6 Go to UniProtKB: S0BBR6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S0BBR6
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
B2 globin chain of giant V2 hemoglobin	C, G	150	Lamellibrachia satsuma	Mutation(s): 0
UniProt
Find proteins for S0BCU7 (Lamellibrachia satsuma) Explore S0BCU7 Go to UniProtKB: S0BCU7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S0BCU7
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
B1 globin chain of giant V2 hemoglobin	D, H	149	Lamellibrachia satsuma	Mutation(s): 0
UniProt
Find proteins for S0BAP9 (Lamellibrachia satsuma) Explore S0BAP9 Go to UniProtKB: S0BAP9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S0BAP9
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Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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	I, J	6		N-Glycosylation	Interactions Focus chain I Focus chain J Interactions & Density Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G64181RO GlyCosmos: G64181RO GlyGen: G64181RO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain Y [auth G] MOL2 format, chain AA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain Y [auth G]	AA [auth H] K [auth A] M [auth B] P [auth C] R [auth D] AA [auth H], K [auth A], M [auth B], P [auth C], R [auth D], T [auth E], V [auth F], Y [auth G]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain Y [auth G]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain X [auth F] MOL2 format, chain O [auth B] MOL2 format, chain X [auth F]	O [auth B], X [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain X [auth F] Interactions & Density Focus chain O [auth B] Focus chain X [auth F]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain Z [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth G]	BA [auth H] L [auth A] N [auth B] Q [auth C] S [auth D] BA [auth H], L [auth A], N [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Z [auth G]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain L [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain L [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.264
R-Value Work: 0.216
R-Value Observed: 0.216
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.556	α = 90
b = 108.556	β = 90
c = 193.552	γ = 120

Software Package:

Software Name	Purpose
BSS	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-06-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-06-04
Type: Initial release
Version 1.1: 2014-08-06
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary

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3WCT

The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: Oxygenated form

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

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Entity ID: 3

UniProt

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Entity ID: 4

UniProt

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Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)