8PIS | pdb_00008pis

Crystal structure of Ser33 in complex with L-Serine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.265 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of Ser33 in complex with L-Serine

Perrone, S.Cifuente, J.O.Marina, A.Mastrella, L.Trastoy, B.Linster, C.L.Guerin, M.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
phosphoglycerate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
473Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SER33
EC: 1.1.1.399 (UniProt), 1.1.1.95 (UniProt)
UniProt
Find proteins for P40510 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40510 
Go to UniProtKB:  P40510
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40510
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
phosphoglycerate dehydrogenase10Saccharomyces cerevisiaeMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
BA [auth F]
CA [auth G]
EA [auth H]
Q [auth A]
S [auth B]
BA [auth F],
CA [auth G],
EA [auth H],
Q [auth A],
S [auth B],
U [auth C],
W [auth D],
Y [auth E]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SER
Query on SER

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth G]
FA [auth H]
R [auth A]
T [auth B]
AA [auth E],
DA [auth G],
FA [auth H],
R [auth A],
T [auth B],
V [auth C],
X [auth D],
Z [auth E]
SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.265 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.115α = 64.42
b = 110.735β = 65.95
c = 117.027γ = 67.03
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Economy and Competitiveness (MINECO)Spain--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release