7CJ2 | pdb_00007cj2

Crystal structure of the Fab antibody complexed with human YKL-40

PDB DOI: https://doi.org/10.2210/pdb7CJ2/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3), Homo sapiens
Mutation(s): No

Deposited: 2020-07-09 Released: 2021-07-14
Deposition Author(s): Choi, S., Na, J.H., Lee, S.J., Woo, J.R., Kim, D.Y., Hong, J.T., Lee, W.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.269 (Depositor), 0.270 (DCC)
R-Value Work:
0.212 (Depositor), 0.217 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the Fab antibody complexed with human YKL-40

Choi, S., Na, J.H., Lee, S.J., Woo, J.R., Kim, D.Y., Lee, W.K.

To be published.

Macromolecule Content

Total Structure Weight: 175.16 kDa
Atom Count: 11,717
Modeled Residue Count: 1,533
Deposited Residue Count: 1,598
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab(Heavy chain)	A [auth C], E [auth K]	222	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab(Light chain)	B [auth D], F [auth L]	215	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase 3-like 1 (Cartilage glycoprotein-39), isoform CRA_a	C [auth A], D [auth B]	362	Homo sapiens	Mutation(s): 0 Gene Names: CHI3L1, hCG_24326
UniProt & NIH Common Fund Data Resources
Find proteins for P36222 (Homo sapiens) Explore P36222 Go to UniProtKB: P36222
PHAROS: P36222 GTEx: ENSG00000133048
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36222
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth A] Focus chain D [auth B]	Go to GlyGen: P36222-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth F]	2		N-Glycosylation	Interactions Focus chain H [auth F] Interactions & Density Focus chain H [auth F]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.269 (Depositor), 0.270 (DCC)
R-Value Work: 0.212 (Depositor), 0.217 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.583	α = 90
b = 132.526	β = 90
c = 160.007	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-07-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-07-14
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary