2CML

Structure of Neuraminidase from English Duck Subtype N6 Complexed with 30 MM ZANAMIVIR, Crystal Soaked for 3 Hours at 291 K.

PDB DOI: https://doi.org/10.2210/pdb2CML/pdb

Classification: HYDROLASE
Organism(s): Influenza A virus
Expression System: Gallus gallus
Mutation(s): No

Deposited: 2006-05-10 Released: 2007-06-05
Deposition Author(s): Rudino-Pinera, E., Tunnah, P., Lukacik, P., Crennell, S.J., Webster, R.G., Laver, W.G., Garman, E.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.180 (Depositor), 0.190 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

The Crystal Structure of Type a Influenza Virus Neuraminidase of the N6 Subtype Reveals the Existence of Two Separate Neu5Ac Binding Sites

Rudino-Pinera, E., Tunnah, P., Crennell, S.J., Webster, R.G., Laver, W.G., Garman, E.F.

To be published.

Macromolecule Content

Total Structure Weight: 181.97 kDa
Atom Count: 13,060
Modelled Residue Count: 1,556
Deposited Residue Count: 1,556
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEURAMINIDASE	A, B, C, D	389	Influenza A virus	Mutation(s): 0 EC: 3.2.1.18
UniProt
Find proteins for Q6XV27 (Influenza A virus (strain A/Duck/England/1/1956 H11N6)) Explore Q6XV27 Go to UniProtKB: Q6XV27
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6XV27
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H, I	2		N-Glycosylation	Interactions Focus chain E Focus chain H Focus chain I Interactions & Density Focus chain E Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose	F	3		N/A	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G00619DD GlyCosmos: G00619DD GlyGen: G00619DD

Entity ID: 4
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)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	5		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G10756ZZ GlyCosmos: G10756ZZ GlyGen: G10756ZZ

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZMR Query on ZMR Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain Z [auth C]	AA [auth C] J [auth A] JA [auth D] K [auth A] KA [auth D] AA [auth C], J [auth A], JA [auth D], K [auth A], KA [auth D], P [auth B], Q [auth B], Z [auth C]	ZANAMIVIR C₁₂ H₂₀ N₄ O₇ ARAIBEBZBOPLMB-UFGQHTETSA-N		Interactions Focus chain AA [auth C] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Z [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	DA [auth C] EA [auth C] FA [auth C] M [auth A] N [auth A] DA [auth C], EA [auth C], FA [auth C], M [auth A], N [auth A], OA [auth D], PA [auth D], S [auth B], T [auth B], U [auth B], V [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	CA [auth C] GA [auth C] HA [auth C] MA [auth D] NA [auth D] CA [auth C], GA [auth C], HA [auth C], MA [auth D], NA [auth D], W [auth B], X [auth B], Y [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain CA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain CA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
BMA Query on BMA Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain O [auth A] SDF format, chain QA [auth D] MOL2 format, chain IA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain QA [auth D] mmCIF format, chain IA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain QA [auth D]	IA [auth C], O [auth A], QA [auth D]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain IA [auth C] Focus chain O [auth A] Focus chain QA [auth D] Interactions & Density Focus chain IA [auth C] Focus chain O [auth A] Focus chain QA [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain R [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain R [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain R [auth B]	BA [auth C], L [auth A], LA [auth D], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain L [auth A] Focus chain LA [auth D] Focus chain R [auth B] Interactions & Density Focus chain BA [auth C] Focus chain L [auth A] Focus chain LA [auth D] Focus chain R [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
ZMR	BindingDB: 2CML	IC50: 23 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.180 (Depositor), 0.190 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.241	α = 90
b = 73.685	β = 90.29
c = 106.684	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-06-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-06-05
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-06-20
Changes: Data collection, Structure summary
Version 1.4: 2019-03-06
Changes: Data collection, Derived calculations, Experimental preparation
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary