3KM0 | pdb_00003km0

17betaHSD1 in complex with 3beta-diol

PDB DOI: https://doi.org/10.2210/pdb3KM0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2009-11-09 Released: 2010-11-10
Deposition Author(s): Mazumdar, M., Lin, S.-X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.312 (Depositor), 0.320 (DCC)
R-Value Work:
0.233 (Depositor), 0.240 (DCC)
R-Value Observed:
0.237 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Molecular basis of sex-steroid translation

Mazumdar, M., Chen, J., Lin, S.-X.

To be published.

Macromolecule Content

Total Structure Weight: 71.85 kDa
Atom Count: 4,544
Modeled Residue Count: 550
Deposited Residue Count: 654
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estradiol 17-beta-dehydrogenase 1	A, B	327	Homo sapiens	Mutation(s): 0 EC: 1.1.1.62 (PDB Primary Data), 1.1.1.51 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P14061 (Homo sapiens) Explore P14061 Go to UniProtKB: P14061
PHAROS: P14061 GTEx: ENSG00000108786
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14061
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
AOM Query on AOM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	5-ALPHA-ANDROSTANE-3-BETA,17BETA-DIOL C₁₉ H₃₂ O₂ CBMYJHIOYJEBSB-YSZCXEEOSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.312 (Depositor), 0.320 (DCC)
R-Value Work: 0.233 (Depositor), 0.240 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.42	α = 90
b = 43.12	β = 128.59
c = 121.1	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
XDS	data scaling
REFMAC	refinement
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-11-10

Deposition Author(s):

Mazumdar, M.

Lin, S.-X.

Revision History (Full details and data files)

Version 1.0: 2010-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 2.0: 2024-03-13
Changes: Advisory, Atomic model, Data collection, Derived calculations

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17betaHSD1 in complex with 3beta-diol

Molecular basis of sex-steroid translation

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations