6A9K | pdb_00006a9k

Crystal structure of the complex of the hydrolytic antibody Fab 9C10 with a transition-state analog

PDB DOI: https://doi.org/10.2210/pdb6A9K/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2018-07-13 Released: 2019-07-24
Deposition Author(s): Tsuchiya, Y., Fujii, I., Tada, T., Yamaguchi, A., Tsumuraya, T., Kumon, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.249 (Depositor), 0.253 (DCC)
R-Value Work:
0.194 (Depositor), 0.201 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of the complex of the hydrolytic antibody Fab 9C10 with a transition-state analog

Tsuchiya, Y., Fujii, I., Tada, T., Yamaguchi, A., Tsumuraya, T., Kumon, A.

To be published.

Macromolecule Content

Total Structure Weight: 97.51 kDa
Atom Count: 7,157
Modeled Residue Count: 878
Deposited Residue Count: 878
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN 9C10 L CHAIN	A [auth L], C [auth A]	219	Mus musculus	Mutation(s): 0

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN 9C10 H CHAIN	B [auth H], D [auth B]	220	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9T0 Query on 9T0 Download:Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain F [auth B] MOL2 format, chain E [auth H] MOL2 format, chain F [auth B] mmCIF format, chain E [auth H] mmCIF format, chain F [auth B]	E [auth H], F [auth B]	5-[(2R,3R)-2-[2,2-bis(chloranyl)ethanoylamino]-3-(4-nitrophenyl)-3-[oxidanyl-[[4-[2,2,2-tris(fluoranyl)ethanoylamino]phenyl]methyl]phosphoryl]oxy-propoxy]-5-oxidanylidene-pentanoic acid C₂₅ H₂₅ Cl₂ F₃ N₃ O₁₁ P DNCOXYFMDXAPCJ-WIYYLYMNSA-N		Interactions Focus chain E [auth H] Focus chain F [auth B] Interactions & Density Focus chain E [auth H] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.249 (Depositor), 0.253 (DCC)
R-Value Work: 0.194 (Depositor), 0.201 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.986	α = 90
b = 36.553	β = 91.5
c = 111.986	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-07-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-07-24
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.