3IEI | pdb_00003iei

Crystal structure of human leucine carboxylmethyltransferase-1 in complex with S-adenosyl homocysteine

PDB DOI: https://doi.org/10.2210/pdb3IEI/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-07-22 Released: 2010-08-11
Deposition Author(s): Xing, Y., Jeffry, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.184 (Depositor), 0.180 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Insights into Novel Functions of a pro-survival PP2A-specific Methyltransferase

Stanevich, V., Jiang, L., Satyshur, K.A., Li, Y., Jeffrey, P.D., Li, Z., Semmelhack, M.F., Xing, Y.

To be published.

Macromolecule Content

Total Structure Weight: 312.63 kDa
Atom Count: 22,201
Modeled Residue Count: 2,480
Deposited Residue Count: 2,672
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine carboxyl methyltransferase 1	A, B, C, D, E A, B, C, D, E, F, G, H	334	Homo sapiens	Mutation(s): 4 Gene Names: CGI-68, LCMT, LCMT-1, LCMT1 EC: 2.1.1 (PDB Primary Data), 2.1.1.233 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIC8 (Homo sapiens) Explore Q9UIC8 Go to UniProtKB: Q9UIC8
PHAROS: Q9UIC8 GTEx: ENSG00000205629
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UIC8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain X [auth G] SDF format, chain V [auth F] SDF format, chain S [auth E] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain Z [auth H] MOL2 format, chain X [auth G] MOL2 format, chain V [auth F] MOL2 format, chain S [auth E] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain Z [auth H] mmCIF format, chain X [auth G] mmCIF format, chain V [auth F] mmCIF format, chain S [auth E] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] N [auth C] P [auth D] S [auth E] I [auth A], K [auth B], N [auth C], P [auth D], S [auth E], V [auth F], X [auth G], Z [auth H]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain Q [auth D] SDF format, chain L [auth B] SDF format, chain AA [auth H] MOL2 format, chain T [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain L [auth B] MOL2 format, chain AA [auth H] mmCIF format, chain T [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain L [auth B] mmCIF format, chain AA [auth H]	AA [auth H], L [auth B], Q [auth D], T [auth E]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain L [auth B] Focus chain Q [auth D] Focus chain T [auth E] Interactions & Density Focus chain AA [auth H] Focus chain L [auth B] Focus chain Q [auth D] Focus chain T [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Y [auth G] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain BA [auth H] MOL2 format, chain Y [auth G] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth H] mmCIF format, chain Y [auth G] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth H]	BA [auth H] J [auth A] M [auth B] O [auth C] R [auth D] BA [auth H], J [auth A], M [auth B], O [auth C], R [auth D], U [auth E], W [auth F], Y [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain BA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]