5C3Y | pdb_00005c3y

Structure of human ribokinase crystallized with AMPPNP

PDB DOI: https://doi.org/10.2210/pdb5C3Y/pdb

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

Deposited: 2015-06-17 Released: 2016-06-15
Deposition Author(s): Park, J., Chakrabarti, J., Singh, B., Gupta, R.S., Junop, M.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.232 (Depositor), 0.234 (DCC)
R-Value Work:
0.205 (Depositor), 0.209 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of human ribokinase crystallized with AMPPNP

Park, J., Chakrabarti, J., Singh, B., Gupta, R.S., Junop, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 428.56 kDa
Atom Count: 28,644
Modeled Residue Count: 3,742
Deposited Residue Count: 3,960
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	330	Homo sapiens	Mutation(s): 0 Gene Names: RBKS, RBSK EC: 2.7.1.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H477 (Homo sapiens) Explore Q9H477 Go to UniProtKB: Q9H477
PHAROS: Q9H477 GTEx: ENSG00000171174
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H477
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AN2 Query on AN2 Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain KA [auth I] SDF format, chain M [auth A] SDF format, chain NA [auth J] SDF format, chain P [auth B] SDF format, chain QA [auth K] SDF format, chain S [auth C] SDF format, chain TA [auth L] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth K] MOL2 format, chain S [auth C] MOL2 format, chain TA [auth L] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain KA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth J] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth K] mmCIF format, chain S [auth C] mmCIF format, chain TA [auth L] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	BA [auth F] EA [auth G] HA [auth H] KA [auth I] M [auth A] BA [auth F], EA [auth G], HA [auth H], KA [auth I], M [auth A], NA [auth J], P [auth B], QA [auth K], S [auth C], TA [auth L], V [auth D], Y [auth E]	AMP PHOSPHORAMIDATE C₁₀ H₁₆ N₆ O₉ P₂ FQMDCEJHLOLKLI-KQYNXXCUSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain QA [auth K] Focus chain S [auth C] Focus chain TA [auth L] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain QA [auth K] Focus chain S [auth C] Focus chain TA [auth L] Focus chain V [auth D] Focus chain Y [auth E]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain LA [auth I] SDF format, chain MA [auth I] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth J] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain RA [auth K] SDF format, chain SA [auth K] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain UA [auth L] SDF format, chain VA [auth L] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth E] SDF format, chain PA [auth J] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain LA [auth I] MOL2 format, chain MA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth K] MOL2 format, chain SA [auth K] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth L] MOL2 format, chain VA [auth L] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain PA [auth J] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain LA [auth I] mmCIF format, chain MA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth J] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth K] mmCIF format, chain SA [auth K] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth L] mmCIF format, chain VA [auth L] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain PA [auth J]	AA [auth E] CA [auth F] DA [auth F] FA [auth G] GA [auth G] AA [auth E], CA [auth F], DA [auth F], FA [auth G], GA [auth G], IA [auth H], JA [auth H], LA [auth I], MA [auth I], N [auth A], O [auth A], OA [auth J], PA [auth J], Q [auth B], R [auth B], RA [auth K], SA [auth K], T [auth C], U [auth C], UA [auth L], VA [auth L], W [auth D], X [auth D], Z [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth J] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth K] Focus chain SA [auth K] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth J] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth K] Focus chain SA [auth K] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.232 (Depositor), 0.234 (DCC)
R-Value Work: 0.205 (Depositor), 0.209 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.31	α = 90
b = 168.14	β = 90.82
c = 161.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-06-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-15
Type: Initial release
Version 1.1: 2017-04-26
Changes: Database references, Structure summary
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description