9L6Q | pdb_00009l6q

Deposited: 2024-12-25 Released: 2025-10-08
Deposition Author(s): Hang, J., Chen, D.D., Zhong, Q.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin K-dependent gamma-carboxylase	A	758	Homo sapiens	Mutation(s): 0 Gene Names: GGCX, GC EC: 4.1.1.90
UniProt & NIH Common Fund Data Resources
Find proteins for P38435 (Homo sapiens) Explore P38435 Go to UniProtKB: P38435
PHAROS: P38435 GTEx: ENSG00000115486
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38435
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: P38435-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	B [auth C]	461	Homo sapiens	Mutation(s): 0 Gene Names: F9 EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens) Explore P00740 Go to UniProtKB: P00740
PHAROS: P00740 GTEx: ENSG00000101981
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00740
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6PL (Subject of Investigation/LOI) Query on 6PL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE C₄₂ H₈₅ N O₈ P PZNPLUBHRSSFHT-RRHRGVEJSA-O		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
1L3 (Subject of Investigation/LOI) Query on 1L3 Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	Menaquinone-4 C₃₁ H₄₀ O₂ DKHGMERMDICWDU-GHDNBGIDSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]