4FMI

Merkel cell polyomavirus VP1 in complex with 3'-sialyllactosamine

PDB DOI: https://doi.org/10.2210/pdb4FMI/pdb

Classification: VIRAL PROTEIN
Organism(s): Merkel cell polyomavirus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-06-17 Released: 2012-09-05
Deposition Author(s): Neu, U., Hengel, H., Stehle, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.236
R-Value Work: 0.196
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 643.35 kDa
Atom Count: 47,100
Modelled Residue Count: 5,474
Deposited Residue Count: 5,780
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	289	Merkel cell polyomavirus	Mutation(s): 0 Gene Names: VP1
UniProt
Find proteins for C0JPK1 (Merkel cell polyomavirus) Explore C0JPK1 Go to UniProtKB: C0JPK1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C0JPK1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	U	3		N/A	Interactions Focus chain U Interactions & Density Focus chain U
Glycosylation Resources
GlyTouCan: G00065MO GlyCosmos: G00065MO GlyGen: G00065MO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose	V	2		N/A	Interactions Focus chain V Interactions & Density Focus chain V
Glycosylation Resources
GlyTouCan: G30207PZ GlyCosmos: G30207PZ GlyGen: G30207PZ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA Query on SIA Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain YA [auth M] MOL2 format, chain EA [auth E] MOL2 format, chain YA [auth M]	EA [auth E], YA [auth M]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain EA [auth E] Focus chain YA [auth M] Interactions & Density Focus chain EA [auth E] Focus chain YA [auth M]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth M] SDF format, chain CA [auth D] SDF format, chain CB [auth N] SDF format, chain EB [auth O] SDF format, chain FA [auth E] SDF format, chain GB [auth P] SDF format, chain HA [auth F] SDF format, chain IB [auth Q] SDF format, chain JA [auth G] SDF format, chain KB [auth R] SDF format, chain LA [auth H] SDF format, chain LB [auth R] SDF format, chain NA [auth I] SDF format, chain NB [auth S] SDF format, chain PA [auth J] SDF format, chain QB [auth T] SDF format, chain RA [auth K] SDF format, chain TA [auth K] SDF format, chain UA [auth L] SDF format, chain VA [auth L] SDF format, chain W [auth A] SDF format, chain WA [auth L] SDF format, chain Y [auth B] SDF format, chain ZA [auth M] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth M] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth N] MOL2 format, chain EB [auth O] MOL2 format, chain FA [auth E] MOL2 format, chain GB [auth P] MOL2 format, chain HA [auth F] MOL2 format, chain IB [auth Q] MOL2 format, chain JA [auth G] MOL2 format, chain KB [auth R] MOL2 format, chain LA [auth H] MOL2 format, chain LB [auth R] MOL2 format, chain NA [auth I] MOL2 format, chain NB [auth S] MOL2 format, chain PA [auth J] MOL2 format, chain QB [auth T] MOL2 format, chain RA [auth K] MOL2 format, chain TA [auth K] MOL2 format, chain UA [auth L] MOL2 format, chain VA [auth L] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth L] MOL2 format, chain Y [auth B] MOL2 format, chain ZA [auth M]	AA [auth C] AB [auth M] CA [auth D] CB [auth N] EB [auth O] AA [auth C], AB [auth M], CA [auth D], CB [auth N], EB [auth O], FA [auth E], GB [auth P], HA [auth F], IB [auth Q], JA [auth G], KB [auth R], LA [auth H], LB [auth R], NA [auth I], NB [auth S], PA [auth J], QB [auth T], RA [auth K], TA [auth K], UA [auth L], VA [auth L], W [auth A], WA [auth L], Y [auth B], ZA [auth M]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth M] Focus chain CA [auth D] Focus chain CB [auth N] Focus chain EB [auth O] Focus chain FA [auth E] Focus chain GB [auth P] Focus chain HA [auth F] Focus chain IB [auth Q] Focus chain JA [auth G] Focus chain KB [auth R] Focus chain LA [auth H] Focus chain LB [auth R] Focus chain NA [auth I] Focus chain NB [auth S] Focus chain PA [auth J] Focus chain QB [auth T] Focus chain RA [auth K] Focus chain TA [auth K] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain W [auth A] Focus chain WA [auth L] Focus chain Y [auth B] Focus chain ZA [auth M] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth M] Focus chain CA [auth D] Focus chain CB [auth N] Focus chain EB [auth O] Focus chain FA [auth E] Focus chain GB [auth P] Focus chain HA [auth F] Focus chain IB [auth Q] Focus chain JA [auth G] Focus chain KB [auth R] Focus chain LA [auth H] Focus chain LB [auth R] Focus chain NA [auth I] Focus chain NB [auth S] Focus chain PA [auth J] Focus chain QB [auth T] Focus chain RA [auth K] Focus chain TA [auth K] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain W [auth A] Focus chain WA [auth L] Focus chain Y [auth B] Focus chain ZA [auth M]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain BB [auth M] SDF format, chain DA [auth D] SDF format, chain DB [auth N] SDF format, chain FB [auth O] SDF format, chain GA [auth E] SDF format, chain HB [auth P] SDF format, chain IA [auth F] SDF format, chain JB [auth Q] SDF format, chain KA [auth G] SDF format, chain MA [auth H] SDF format, chain MB [auth R] SDF format, chain OA [auth I] SDF format, chain OB [auth S] SDF format, chain PB [auth S] SDF format, chain QA [auth J] SDF format, chain RB [auth T] SDF format, chain SA [auth K] SDF format, chain X [auth A] SDF format, chain XA [auth L] SDF format, chain Z [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth M] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth N] MOL2 format, chain FB [auth O] MOL2 format, chain GA [auth E] MOL2 format, chain HB [auth P] MOL2 format, chain IA [auth F] MOL2 format, chain JB [auth Q] MOL2 format, chain KA [auth G] MOL2 format, chain MA [auth H] MOL2 format, chain MB [auth R] MOL2 format, chain OA [auth I] MOL2 format, chain OB [auth S] MOL2 format, chain PB [auth S] MOL2 format, chain QA [auth J] MOL2 format, chain RB [auth T] MOL2 format, chain SA [auth K] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth L] MOL2 format, chain Z [auth B]	BA [auth C] BB [auth M] DA [auth D] DB [auth N] FB [auth O] BA [auth C], BB [auth M], DA [auth D], DB [auth N], FB [auth O], GA [auth E], HB [auth P], IA [auth F], JB [auth Q], KA [auth G], MA [auth H], MB [auth R], OA [auth I], OB [auth S], PB [auth S], QA [auth J], RB [auth T], SA [auth K], X [auth A], XA [auth L], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain BB [auth M] Focus chain DA [auth D] Focus chain DB [auth N] Focus chain FB [auth O] Focus chain GA [auth E] Focus chain HB [auth P] Focus chain IA [auth F] Focus chain JB [auth Q] Focus chain KA [auth G] Focus chain MA [auth H] Focus chain MB [auth R] Focus chain OA [auth I] Focus chain OB [auth S] Focus chain PB [auth S] Focus chain QA [auth J] Focus chain RB [auth T] Focus chain SA [auth K] Focus chain X [auth A] Focus chain XA [auth L] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth C] Focus chain BB [auth M] Focus chain DA [auth D] Focus chain DB [auth N] Focus chain FB [auth O] Focus chain GA [auth E] Focus chain HB [auth P] Focus chain IA [auth F] Focus chain JB [auth Q] Focus chain KA [auth G] Focus chain MA [auth H] Focus chain MB [auth R] Focus chain OA [auth I] Focus chain OB [auth S] Focus chain PB [auth S] Focus chain QA [auth J] Focus chain RB [auth T] Focus chain SA [auth K] Focus chain X [auth A] Focus chain XA [auth L] Focus chain Z [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900067 Query on PRD_900067	U	3'-sialyl-N-acetyllactosamine	Oligosaccharide / Substrate analog		Interactions Focus chain U Interactions & Density Focus chain U

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.236
R-Value Work: 0.196
R-Value Observed: 0.196
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.04	α = 93.02
b = 85.7	β = 100.41
c = 248.73	γ = 108.07

Software Package:

Software Name	Purpose
RemDAq	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-05

Deposition Author(s):

Neu, U.

Hengel, H.

Stehle, T.

Revision History (Full details and data files)

Version 1.0: 2012-09-05
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary