4CR7

Crystal structure of the N-acetyl-D-mannosamine dehydrogenase with n-acetylmannosamine

PDB DOI: https://doi.org/10.2210/pdb4CR7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Flavobacterium sp. 141-8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-02-25 Released: 2014-07-09
Deposition Author(s): Gil-Ortiz, F., Sola-Carvajal, A., Garcia-Carmona, F., Sanchez-Ferrer, A., Rubio, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.231
R-Value Work: 0.201
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 446.9 kDa
Atom Count: 30,349
Modelled Residue Count: 4,147
Deposited Residue Count: 4,336
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ACYLMANNOSAMINE 1-DEHYDROGENASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	271	Flavobacterium sp. 141-8	Mutation(s): 0 EC: 1.1.1.233
UniProt
Find proteins for P22441 (Flavobacterium sp. (strain 141-8)) Explore P22441 Go to UniProtKB: P22441
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22441
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BM3 Query on BM3 Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain GA [auth G] SDF format, chain IA [auth H] SDF format, chain KA [auth I] SDF format, chain MA [auth J] SDF format, chain OA [auth K] SDF format, chain PA [auth L] SDF format, chain QA [auth M] SDF format, chain R [auth A] SDF format, chain SA [auth N] SDF format, chain T [auth B] SDF format, chain U [auth C] SDF format, chain UA [auth O] SDF format, chain V [auth D] SDF format, chain WA [auth P] SDF format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain MA [auth J] MOL2 format, chain OA [auth K] MOL2 format, chain PA [auth L] MOL2 format, chain QA [auth M] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth N] MOL2 format, chain T [auth B] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth O] MOL2 format, chain V [auth D] MOL2 format, chain WA [auth P] MOL2 format, chain Y [auth E]	CA [auth F] GA [auth G] IA [auth H] KA [auth I] MA [auth J] CA [auth F], GA [auth G], IA [auth H], KA [auth I], MA [auth J], OA [auth K], PA [auth L], QA [auth M], R [auth A], SA [auth N], T [auth B], U [auth C], UA [auth O], V [auth D], WA [auth P], Y [auth E]	2-acetamido-2-deoxy-alpha-D-mannopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-UOLFYFMNSA-N		Interactions Focus chain CA [auth F] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain PA [auth L] Focus chain QA [auth M] Focus chain R [auth A] Focus chain SA [auth N] Focus chain T [auth B] Focus chain U [auth C] Focus chain UA [auth O] Focus chain V [auth D] Focus chain WA [auth P] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain PA [auth L] Focus chain QA [auth M] Focus chain R [auth A] Focus chain SA [auth N] Focus chain T [auth B] Focus chain U [auth C] Focus chain UA [auth O] Focus chain V [auth D] Focus chain WA [auth P] Focus chain Y [auth E]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain FA [auth G] SDF format, chain HA [auth H] SDF format, chain JA [auth I] SDF format, chain LA [auth J] SDF format, chain NA [auth K] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain VA [auth P] SDF format, chain X [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain JA [auth I] MOL2 format, chain LA [auth J] MOL2 format, chain NA [auth K] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain VA [auth P] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth F]	AA [auth F] BA [auth F] DA [auth F] EA [auth F] FA [auth G] AA [auth F], BA [auth F], DA [auth F], EA [auth F], FA [auth G], HA [auth H], JA [auth I], LA [auth J], NA [auth K], Q [auth A], S [auth B], VA [auth P], X [auth E], Z [auth F]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain JA [auth I] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain Q [auth A] Focus chain S [auth B] Focus chain VA [auth P] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain JA [auth I] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain Q [auth A] Focus chain S [auth B] Focus chain VA [auth P] Focus chain X [auth E] Focus chain Z [auth F]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain RA [auth M] SDF format, chain TA [auth N] SDF format, chain W [auth D] SDF format, chain XA [auth P] MOL2 format, chain RA [auth M] MOL2 format, chain TA [auth N] MOL2 format, chain W [auth D] MOL2 format, chain XA [auth P]	RA [auth M], TA [auth N], W [auth D], XA [auth P]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain RA [auth M] Focus chain TA [auth N] Focus chain W [auth D] Focus chain XA [auth P] Interactions & Density Focus chain RA [auth M] Focus chain TA [auth N] Focus chain W [auth D] Focus chain XA [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.231
R-Value Work: 0.201
R-Value Observed: 0.202
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.39	α = 67.43
b = 100.12	β = 89.75
c = 111.6	γ = 72.46

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-09
Type: Initial release
Version 1.1: 2014-09-03
Changes: Atomic model, Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary