5MKN | pdb_00005mkn

Crystal structure of SmAP (LSm) protein from Methanococcus vannielii

PDB DOI: https://doi.org/10.2210/pdb5MKN/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Methanococcus vannielii
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2016-12-05 Released: 2017-12-20
Deposition Author(s): Nikulin, A.D., Lekontseva, N.V., Tishchenko, S.V., Kravchenko, O.V.
Funding Organization(s): Russian Scientific Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.315 (Depositor), 0.310 (DCC)
R-Value Work:
0.233 (Depositor), 0.230 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of SmAP (LSm) protein from Methanococcus vannielii in complex with URIDINE-5'-MONOPHOSPHATE

Nikulin, A.D., Lekontseva, N.V., Tishchenko, S.V., Kravchenko, O.V.

To be published.

Macromolecule Content

Total Structure Weight: 239.88 kDa
Atom Count: 16,173
Modeled Residue Count: 1,962
Deposited Residue Count: 2,016
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Like-Sm ribonucleoprotein core	A AA [auth b] B BA [auth d] C A, AA [auth b], B, BA [auth d], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	72	Methanococcus vannielii	Mutation(s): 0 Gene Names: Mevan_0470
UniProt
Find proteins for A6UPF5 (Methanococcus vannielii (strain ATCC 35089 / DSM 1224 / JCM 13029 / OCM 148 / SB)) Explore A6UPF5 Go to UniProtKB: A6UPF5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6UPF5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U5P Query on U5P Download Ideal Coordinates CCD File SDF format, chain ZA [auth Q] SDF format, chain YA [auth P] SDF format, chain XA [auth O] SDF format, chain WA [auth N] SDF format, chain UA [auth M] SDF format, chain TA [auth L] SDF format, chain SA [auth K] SDF format, chain QA [auth J] SDF format, chain PA [auth I] SDF format, chain OB [auth d] SDF format, chain OA [auth H] SDF format, chain MB [auth b] SDF format, chain MA [auth G] SDF format, chain LB [auth a] SDF format, chain LA [auth F] SDF format, chain KA [auth F] SDF format, chain JB [auth Z] SDF format, chain IB [auth Y] SDF format, chain IA [auth E] SDF format, chain HB [auth X] SDF format, chain GA [auth D] SDF format, chain FB [auth W] SDF format, chain FA [auth C] SDF format, chain EB [auth V] SDF format, chain DB [auth U] SDF format, chain DA [auth B] SDF format, chain CB [auth U] SDF format, chain CA [auth A] SDF format, chain BB [auth T] SDF format, chain AB [auth R] MOL2 format, chain ZA [auth Q] MOL2 format, chain YA [auth P] MOL2 format, chain XA [auth O] MOL2 format, chain WA [auth N] MOL2 format, chain UA [auth M] MOL2 format, chain TA [auth L] MOL2 format, chain SA [auth K] MOL2 format, chain QA [auth J] MOL2 format, chain PA [auth I] MOL2 format, chain OB [auth d] MOL2 format, chain OA [auth H] MOL2 format, chain MB [auth b] MOL2 format, chain MA [auth G] MOL2 format, chain LB [auth a] MOL2 format, chain LA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain JB [auth Z] MOL2 format, chain IB [auth Y] MOL2 format, chain IA [auth E] MOL2 format, chain HB [auth X] MOL2 format, chain GA [auth D] MOL2 format, chain FB [auth W] MOL2 format, chain FA [auth C] MOL2 format, chain EB [auth V] MOL2 format, chain DB [auth U] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth U] MOL2 format, chain CA [auth A] MOL2 format, chain BB [auth T] MOL2 format, chain AB [auth R] mmCIF format, chain ZA [auth Q] mmCIF format, chain YA [auth P] mmCIF format, chain XA [auth O] mmCIF format, chain WA [auth N] mmCIF format, chain UA [auth M] mmCIF format, chain TA [auth L] mmCIF format, chain SA [auth K] mmCIF format, chain QA [auth J] mmCIF format, chain PA [auth I] mmCIF format, chain OB [auth d] mmCIF format, chain OA [auth H] mmCIF format, chain MB [auth b] mmCIF format, chain MA [auth G] mmCIF format, chain LB [auth a] mmCIF format, chain LA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain JB [auth Z] mmCIF format, chain IB [auth Y] mmCIF format, chain IA [auth E] mmCIF format, chain HB [auth X] mmCIF format, chain GA [auth D] mmCIF format, chain FB [auth W] mmCIF format, chain FA [auth C] mmCIF format, chain EB [auth V] mmCIF format, chain DB [auth U] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth U] mmCIF format, chain CA [auth A] mmCIF format, chain BB [auth T] mmCIF format, chain AB [auth R]	AB [auth R] BB [auth T] CA [auth A] CB [auth U] DA [auth B] AB [auth R], BB [auth T], CA [auth A], CB [auth U], DA [auth B], DB [auth U], EB [auth V], FA [auth C], FB [auth W], GA [auth D], HB [auth X], IA [auth E], IB [auth Y], JB [auth Z], KA [auth F], LA [auth F], LB [auth a], MA [auth G], MB [auth b], OA [auth H], OB [auth d], PA [auth I], QA [auth J], SA [auth K], TA [auth L], UA [auth M], WA [auth N], XA [auth O], YA [auth P], ZA [auth Q]	URIDINE-5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₉ P DJJCXFVJDGTHFX-XVFCMESISA-N		Interactions Focus chain AB [auth R] Focus chain BB [auth T] Focus chain CA [auth A] Focus chain CB [auth U] Focus chain DA [auth B] Focus chain DB [auth U] Focus chain EB [auth V] Focus chain FA [auth C] Focus chain FB [auth W] Focus chain GA [auth D] Focus chain HB [auth X] Focus chain IA [auth E] Focus chain IB [auth Y] Focus chain JB [auth Z] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain LB [auth a] Focus chain MA [auth G] Focus chain MB [auth b] Focus chain OA [auth H] Focus chain OB [auth d] Focus chain PA [auth I] Focus chain QA [auth J] Focus chain SA [auth K] Focus chain TA [auth L] Focus chain UA [auth M] Focus chain WA [auth N] Focus chain XA [auth O] Focus chain YA [auth P] Focus chain ZA [auth Q] Interactions & Density Focus chain AB [auth R] Focus chain BB [auth T] Focus chain CA [auth A] Focus chain CB [auth U] Focus chain DA [auth B] Focus chain DB [auth U] Focus chain EB [auth V] Focus chain FA [auth C] Focus chain FB [auth W] Focus chain GA [auth D] Focus chain HB [auth X] Focus chain IA [auth E] Focus chain IB [auth Y] Focus chain JB [auth Z] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain LB [auth a] Focus chain MA [auth G] Focus chain MB [auth b] Focus chain OA [auth H] Focus chain OB [auth d] Focus chain PA [auth I] Focus chain QA [auth J] Focus chain SA [auth K] Focus chain TA [auth L] Focus chain UA [auth M] Focus chain WA [auth N] Focus chain XA [auth O] Focus chain YA [auth P] Focus chain ZA [auth Q]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain VA [auth M] SDF format, chain RA [auth J] SDF format, chain PB [auth d] SDF format, chain NB [auth b] SDF format, chain NA [auth G] SDF format, chain KB [auth Z] SDF format, chain JA [auth E] SDF format, chain HA [auth D] SDF format, chain GB [auth W] SDF format, chain EA [auth B] MOL2 format, chain VA [auth M] MOL2 format, chain RA [auth J] MOL2 format, chain PB [auth d] MOL2 format, chain NB [auth b] MOL2 format, chain NA [auth G] MOL2 format, chain KB [auth Z] MOL2 format, chain JA [auth E] MOL2 format, chain HA [auth D] MOL2 format, chain GB [auth W] MOL2 format, chain EA [auth B] mmCIF format, chain VA [auth M] mmCIF format, chain RA [auth J] mmCIF format, chain PB [auth d] mmCIF format, chain NB [auth b] mmCIF format, chain NA [auth G] mmCIF format, chain KB [auth Z] mmCIF format, chain JA [auth E] mmCIF format, chain HA [auth D] mmCIF format, chain GB [auth W] mmCIF format, chain EA [auth B]	EA [auth B] GB [auth W] HA [auth D] JA [auth E] KB [auth Z] EA [auth B], GB [auth W], HA [auth D], JA [auth E], KB [auth Z], NA [auth G], NB [auth b], PB [auth d], RA [auth J], VA [auth M]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain GB [auth W] Focus chain HA [auth D] Focus chain JA [auth E] Focus chain KB [auth Z] Focus chain NA [auth G] Focus chain NB [auth b] Focus chain PB [auth d] Focus chain RA [auth J] Focus chain VA [auth M] Interactions & Density Focus chain EA [auth B] Focus chain GB [auth W] Focus chain HA [auth D] Focus chain JA [auth E] Focus chain KB [auth Z] Focus chain NA [auth G] Focus chain NB [auth b] Focus chain PB [auth d] Focus chain RA [auth J] Focus chain VA [auth M]