6NKF | pdb_00006nkf

Crystal Structure of the Lipase Lip_vut4 from Goat Rumen metagenome.

PDB DOI: https://doi.org/10.2210/pdb6NKF/pdb

Classification: HYDROLASE
Organism(s): metagenome
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-01-07 Released: 2020-01-22
Deposition Author(s): Kim, Y., Welk, L., Mukendi, G., Nkhi, G., Motloi, T., Jedrzejczak, R., Feto, N., Joachimiak, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.179 (Depositor), 0.180 (DCC)
R-Value Work:
0.153 (Depositor), 0.150 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the Lipase Lip_vut4 from Goat Rumen metagenome.

Kim, Y., Welk, L., Jedrzejczak, R., Feto, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 139.63 kDa
Atom Count: 10,338
Modeled Residue Count: 1,192
Deposited Residue Count: 1,216
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lip_vut4, C3L	A, B, C, D	304	metagenome	Mutation(s): 0
UniProt
Find proteins for Q65FG3 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65FG3 Go to UniProtKB: Q65FG3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q65FG3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C]	F [auth A], M [auth B], S [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain S [auth C]
SBT Query on SBT Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	2-BUTANOL C₄ H₁₀ O BTANRVKWQNVYAZ-BYPYZUCNSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] E [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth D], E [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D]