5T2U

short chain dehydrogenase/reductase family protein

> 概要

5T2U の概要

分子名称Oxidoreductase, short chain dehydrogenase/reductase family protein, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (3 entities in total)
機能のキーワードfabg, mycobacterium, fatty acids, oxidoreductase
由来する生物種Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
ポリマー鎖数4
分子量合計105391.52
構造登録者
Mickael, B.,Van Wyk, N.,Baneres-Roquet, F.,Yann, G.,Laurent, K. (登録日: 2016-08-24, 公開日: 2017-02-15, 最終更新日: 2017-03-22)
主引用文献
Blaise, M.,Van Wyk, N.,Baneres-Roquet, F.,Guerardel, Y.,Kremer, L.
Binding of NADP(+) triggers an open-to-closed transition in a mycobacterial FabG beta-ketoacyl-ACP reductase.
Biochem. J., 474:907-921, 2017
PubMed: 28126742 (主引用文献が同じPDBエントリー)
DOI: 10.1042/BCJ20161052
MImport into Mendeley
実験手法
X-RAY DIFFRACTION (2.2 Å)
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構造検証レポート

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.218100.9%1.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution
検証レポート(詳細版)をダウンロード

他の静止画像(非対称単位)

Molmil generated image of 5t2u
回転なし
Molmil generated image of 5t2u
x軸(左右方向)周りに90°回転
Molmil generated image of 5t2u
y軸(上下方向)周りに90°回転

> 構造情報

エンティティ

鎖名説明種類鎖長分子量分子数データベース名(アクセス番号)由来する生物種エンティティの一般名
A, B, C, DOxidoreductase, short chain dehydrogenase/reductase family proteinpolymer24825604.54
UniProt (A0R723)
Pfam (PF00106)
Pfam (PF01370)
Pfam (PF02719)
Pfam (PF08659)
Pfam (PF13561)
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Short-chain dehydrogenase/reductase SDR
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATEnon-polymer743.44
waterwater18.0738

配列ビューア

非対称単位の内容

ポリマー鎖の数4
分子量合計102417.9
非ポリマー*分子数4
分子量合計2973.6
全て*分子量合計105391.5
*水分子は含んでいません

> 実験情報

精密化の統計情報

実験手法:X-RAY DIFFRACTION (2.2 Å)

格子定数 [Å]65.010116.110132.870
格子定数 [度]90.0090.0090.00
空間群P 21 21 21
分解能 [Å] (低 - 高)19.91 - 2.20
最も高い分解能シェルの値2.255 - 2.200
R因子0.1651
R-work0.16300
最も高い分解能シェルの値0.232
R-free0.21770
最も高い分解能シェルの値0.278
結合長の平均二乗偏差(RMSD) [Å]0.003
結合角の平均二乗偏差(RMSD) [度]0.693

回折データの統計情報

分解能 [Å] (低 - 高)19.91 - 2.20
最も高い分解能シェルの値 -
独立反射数51201
完全性 [%]98.7
冗長性3.7
最も高い分解能シェルの値3.7

結晶化条件

結晶ID方法pHpHの範囲温度単位
1VAPOR DIFFUSION, SITTING DROP291

結晶化試薬

ID結晶ID濃度試薬名濃度 (単位)詳細
文献の結晶化試薬*
ID結晶ID溶液試薬名濃度 (単位) (単位)詳細
注釈情報は下記文献より抽出しています*

> 機能情報

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GO(遺伝子オントロジー)由来の情報

鎖名GO(遺伝子オントロジー)id名前空間内容
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PDBデータベースに由来する情報

site_id残基数詳細
AC136binding site for residue NAP A 301
鎖名残基
AGLY12
ATHR14
ASER15
AGLY16
AILE17
AGLY36
AARG37
AASP38
AARG41
AALA58
AASP59
ALEU60
AASN82
ATYR86
ATHR105
AILE132
ATHR133
ATHR134
ATYR147
ALYS151
APRO177
AGLY178
APRO179
ATHR180
ATHR182
ATHR184
ATHR185
AHOH408
AHOH412
AHOH413
AHOH417
AHOH468
AHOH494
AHOH502
AHOH505
AHOH509

AC232binding site for residue NAP B 301
鎖名残基
BGLY12
BTHR14
BSER15
BGLY16
BILE17
BARG37
BASP38
BARG41
BALA58
BASP59
BLEU60
BASN82
BTYR86
BTHR105
BILE132
BTHR133
BTHR134
BTYR147
BLYS151
BPRO177
BGLY178
BPRO179
BTHR180
BTHR182
BTHR184
BTHR185
BHOH401
BHOH427
BHOH436
BHOH451
BHOH477
BHOH485

AC330binding site for residue NAP C 301
鎖名残基
CGLY12
CTHR14
CSER15
CGLY16
CILE17
CARG37
CASP38
CARG41
CALA58
CASP59
CLEU60
CASN82
CGLY84
CTYR86
CTHR105
CILE132
CTHR133
CTHR134
CTYR147
CLYS151
CPRO177
CGLY178
CTHR180
CTHR182
CTHR184
CTHR185
CHOH445
CHOH467
CHOH486
CHOH510

AC428binding site for residue NAP D 301
鎖名残基
DGLY12
DTHR14
DSER15
DGLY16
DILE17
DARG37
DASP38
DARG41
DALA58
DASP59
DLEU60
DASN82
DTYR86
DTHR105
DILE132
DTHR133
DTHR134
DTYR147
DLYS151
DPRO177
DGLY178
DTHR180
DTHR182
DTHR184
DTHR185
DHOH402
DHOH421
DHOH431

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「HETATM」原子の座標から抽出されたリガンド結合部位

site_id残基数詳細
NAP_5t2u_A_30137NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE binding site
鎖名残基ligand
AGLY12-GLY18NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ATHR35-ASP38NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AARG41NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AALA58-GLY61NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AASN82-TYR86NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ATHR105NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AILE132-LEU135NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ATYR147NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ALYS151NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
APRO177-THR180NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ATHR182-THR185NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AILE193NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

NAP_5t2u_B_30135NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE binding site
鎖名残基ligand
BGLY12-GLY18NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BTHR35-ASP38NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BARG41NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BALA58-GLY61NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BASN82-TYR86NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BTHR105NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BILE132-THR134NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BTYR147NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BLYS151NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BPRO177-THR180NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BTHR182-THR185NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

NAP_5t2u_C_30137NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE binding site
鎖名残基ligand
CGLY12-GLY18NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CTHR35-ASP38NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CARG41NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CALA58-GLY61NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CASN82-TYR86NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CTHR105NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CILE132-LEU135NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CTYR147NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CLYS151NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CPRO177-THR180NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CTHR182-THR185NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CILE193NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

NAP_5t2u_D_30137NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE binding site
鎖名残基ligand
DGLY12-GLY18NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DTHR35-ASP38NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DARG41NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DALA58-GLY61NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DASN82-TYR86NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DTHR105NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DILE132-LEU135NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DTYR147NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DLYS151NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DPRO177-THR180NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DTHR182-THR185NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DILE193NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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UniProtにおけるモチーフ・データベースPROSITEからの機能情報

site_id残基数詳細
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SwissProt/UniProtに記載されている蛋白質分子機能情報

site_id残基数詳細
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CSAにおける酵素触媒機能の情報

site_id残基数詳細

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