◆ コラーゲンの例（Jmol版） ◆

　PDBj「今月の分子」から商品広告でもよく目にするコラーゲン。骨，腱，皮膚などを形成している硬タンパク質の一種で，3本のタンパク質が三つ編みのようになっている三重ヘリックスでできているのが強さの秘密です。種類によってアミノ酸組成などが異なりますが，グリシン（Gly）を周期的に含み，プロリン（Pro）やヒドロキシプロリン（Hyp）も特徴的に含まれます。


 1bkv（コラーゲン様モデルペプチド T3-785）
7cwk（ヒトのコラーゲンtype I）
8k4wのChain A・B・C（ヒトのコラーゲンtype I）
9gtu（ヒトのコラーゲンtype IV α1・α2・α3）　→ Collagen VI microfibril structure reveals mechanism for molecular assembly and clustering of inherited pathogenic mutations（Nature Communications，2025/08/14）　［Collagen, type VI, alpha 1 - Wikipedia，同 alpha 2 - Wikipedia，同 alpha 3 - Wikipedia］
9lrm（分解前のヒトのコラーゲンに結合した細菌のコラゲナーゼH，E416Q変異体）　Chain B-D（コラーゲン）選択　［Collagenase - Wikipedia］
1cag（コラーゲン様ペプチド）
バックボーン　二次構造
全選択　タンパク質選択　リガンド選択
Gly選択　Pro選択　ヒドロキシPro選択　Cys選択
 空間充填　球棒　球60％　スティック　針金　消去
アミノ色　Chain色　CPK色　‖　Jmol色　Rasmol色
濃赤　濃青　緑　ピンク　濃ピンク　橙　紫

糖鎖別着色（#印のみ）：Gal，α-Glc，β-Glc，Man，Fuc，Xyl，Sia，GalNAc，GlcNAc，GlcA
酸性・中性・塩基性区別　極性・非極性区別
疎水性インデックス順　I/O値順（特性基 R）　等電点順
コンホメーション選択性（αヘリックス・βストランド）#
ヒトの必須・非必須区別
 水素結合（太）　OFF
　
　
背景・黒　灰　白　紺


●：Gly　●：Pro　●：ヒドロキシPro
参考：1BKVのアミノ酸配列；3残基ごとに改行
着色はアミノ色，およびHyp（ヒドロキシPro）
※Sequence：PXGPXGPXGITGARGLAGPXGPXGPXGPXG（Chain A・B・C共通）
FASTA配列は PPGPPGPPGITGARGLAGPPGPPGPPGPPG
Pro Hyp Gly
Pro Hyp Gly
Pro Hyp Gly
Ile Thr Gly
Ala Arg Gly
Leu Ala Gly
Pro Hyp Gly
Pro Hyp Gly
Pro Hyp Gly
Pro Hyp Gly
コラーゲン様モデルペプチド T3-785の例 1bkv


●：Gly　●：Pro　●：ヒドロキシPro
参考：7CWKのアミノ酸配列；3残基ごとに改行
着色は有機概念図I/O値順（特性基 R）
FASTA配列は XPPGPPGPPGQRGERGFPGPPGPPGPPG（Chain A・B・C共通）
   
X
Pro Pro Gly
Pro Pro Gly
Pro Pro Gly
Gln Arg Gly
Glu Arg Gly
Phe Pro Gly
Pro Pro Gly
Pro Pro Gly
Pro Pro Gly
ヒトのコラーゲンtype Iの例 7cwk

参考：9LRMのChain B・C・Dのアミノ酸配列；3残基ごとに改行
着色は有機概念図I/O値順（特性基 R）
FASTA配列は PPGPPGPPGPPGPPGPPGPPGPPGPPGPPG（Chain B・C・D共通）
Pro Pro Gly
Pro Pro Gly
Pro Pro Gly
Pro Pro Gly
Pro Pro Gly
Pro Pro Gly
Pro Pro Gly
Pro Pro Gly
Pro Pro Gly
Pro Pro Gly
分解前のヒトのコラーゲンに結合した細菌のコラゲナーゼH 9lrm

参考：8K4Wのアミノ酸配列；3残基ごとに改行
着色は有機概念図I/O値順（特性基 R）
FASTA配列は XPPGPPGPPGQRGERGFPGPPGPPGPPG
（Chain A〜L共通〈上掲データはChain A・B・C〉でこの配列が各Chainでそれぞれ10回ほど繰り返し）
Pro Pro Gly
Pro Pro Gly
Pro Pro Gly
Ala Arg Gly
Glu Arg Gly
Phe Pro Gly
Glu Arg Gly
Pro Pro Gly
Pro Pro Gly
Pro Pro Gly
ヒトのコラーゲンtype Iの例 8k4w

alpha 1
Asp Tyr Lys Asp Asp Asp Asp Lys Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser Gly Pro Pro Gly Ile Val Gly Gln Lys Gly Arg Pro Gly Tyr Pro Gly Pro Ala Gly Pro Arg Gly Asn Arg Gly Asp Ser Ile Asp Gln Cys Ala
Leu Ile Gln Ser Ile Lys Asp Lys Cys Pro Cys Cys Tyr Gly Pro Leu Glu Cys Pro Val Phe Pro Thr Glu Leu Ala Phe Ala Leu Asp Thr Ser Glu Gly Val Asn Gln Asp Thr Phe Gly Arg Met Arg Asp Val Val Leu Ser Ile
Val Asn Val Leu Thr Ile Ala Glu Ser Asn Cys Pro Thr Gly Ala Arg Val Ala Val Val Thr Tyr Asn Asn Glu Val Thr Thr Glu Ile Arg Phe Ala Asp Ser Lys Arg Lys Ser Val Leu Leu Asp Lys Ile Lys Asn Leu Gln Val
Ala Leu Thr Ser Lys Gln Gln Ser Leu Glu Thr Ala Met Ser Phe Val Ala Arg Asn Thr Phe Lys Arg Val Arg Asn Gly Phe Leu Met Arg Lys Val Ala Val Phe Phe Ser Asn Thr Pro Thr Arg Ala Ser Pro Gln Leu Arg Glu
Ala Val Leu Lys Leu Ser Asp Ala Gly Ile Thr Pro Leu Phe Leu Thr Arg Gln Glu Asp Arg Gln Leu Ile Asn Ala Leu Gln Ile Asn Asn Thr Ala Val Gly His Ala Leu Val Leu Pro Ala Gly Arg Asp Leu Thr Asp Phe Leu
Glu Asn Val Leu Thr Cys His Val Cys Leu Asp Ile Cys Asn Ile Asp Pro Ser Cys Gly Phe Gly Ser Trp Arg Pro Ser Phe Arg Asp Ala Ala Ala Ala Gly Ser Asp Val Asp Ile Asp Met Ala Phe Ile Leu Asp Ser Ala Glu
Thr Thr Thr Leu Phe Gln Phe Asn Glu Met Lys Lys Tyr Ile Ala Tyr Leu Val Arg Gln Leu Asp Met Ser Pro Asp Pro Lys Ala Ser Gln His Phe Ala Arg Val Ala Val Val Gln His Ala Pro Ser Glu Ser Val Asp Asn Ala
Ser Met Pro Pro Val Lys Val Glu Phe Ser Leu Thr Asp Tyr Gly Ser Lys Glu Lys Leu Val Asp Phe Leu Ser Arg Gly Met Thr Gln Leu Gln Gly Thr Arg Ala Leu Gly Ser Ala Ile Glu Tyr Thr Ile Glu Asn Val Phe Glu
Ser Ala Pro Asn Pro Arg Asp Leu Lys Ile Val Val Leu Met Leu Thr Gly Glu Val Pro Glu Gln Gln Leu Glu Glu Ala Gln Arg Val Ile Leu Gln Ala Lys Cys Lys Gly Tyr Phe Phe Val Val Leu Gly Ile Gly Arg Lys Val
Asn Ile Lys Glu Val Tyr Thr Phe Ala Ser Glu Pro Asn Asp Val Phe Phe Lys Leu Val Asp Lys Ser Thr Glu Leu Asn Glu Glu Pro Leu Met Arg Phe Gly Arg Leu Leu Pro Ser Phe Val
alpha 2
Ser Ala Trp Ser His Pro Gln Phe Glu Lys Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser Gly Glu Pro Gly Pro Arg Gly Pro Arg Gly Val Pro Gly Pro Glu Gly Glu Pro Gly Pro Pro Gly Asp Pro Gly Leu Thr Glu Cys Asp
Val Met Thr Tyr Val Arg Glu Thr Cys Gly Cys Cys Asp Cys Glu Lys Arg Cys Gly Ala Leu Asp Val Val Phe Val Ile Asp Ser Ser Glu Ser Ile Gly Tyr Thr Asn Phe Thr Leu Glu Lys Asn Phe Val Ile Asn Val Val Asn
Arg Leu Gly Ala Ile Ala Lys Asp Pro Lys Ser Glu Thr Gly Thr Arg Val Gly Val Val Gln Tyr Ser His Glu Gly Thr Phe Glu Ala Ile Gln Leu Asp Asp Glu His Ile Asp Ser Leu Ser Ser Phe Lys Glu Ala Val Lys Asn
Leu Glu Trp Ile Ala Gly Gly Thr Trp Thr Pro Ser Ala Leu Lys Phe Ala Tyr Asp Arg Leu Ile Lys Glu Ser Arg Arg Gln Lys Thr Arg Val Phe Ala Val Val Ile Thr Asp Gly Arg His Asp Pro Arg Asp Asp Asp Leu Asn
Leu Arg Ala Leu Cys Asp Arg Asp Val Thr Val Thr Ala Ile Gly Ile Gly Asp Met Phe His Glu Lys His Glu Ser Glu Asn Leu Tyr Ser Ile Ala Cys Asp Lys Pro Gln Gln Val Arg Asn Met Thr Leu Phe Ser Asp Leu Val
Ala Glu Lys Phe Ile Asp Asp Met Glu Asp Val Leu Cys Pro Asp Pro Gln Ile Val Cys Pro Asp Leu Pro Cys Gln Thr Glu Leu Ser Val Ala Gln Cys Thr Gln Arg Pro Val Asp Ile Val Phe Leu Leu Asp Gly Ser Glu Arg
Leu Gly Glu Gln Asn Phe His Lys Ala Arg Arg Phe Val Glu Gln Val Ala Arg Arg Leu Thr Leu Ala Arg Arg Asp Asp Asp Pro Leu Asn Ala Arg Val Ala Leu Leu Gln Phe Gly Gly Pro Gly Glu Gln Gln Val Ala Phe Pro
Leu Ser His Asn Leu Thr Ala Ile His Glu Ala Leu Glu Thr Thr Gln Tyr Leu Asn Ser Phe Ser His Val Gly Ala Gly Val Val His Ala Ile Asn Ala Ile Val Arg Ser Pro Arg Gly Gly Ala Arg Arg His Ala Glu Leu Ser
Phe Val Phe Leu Thr Asp Gly Val Thr Gly Asn Asp Ser Leu His Glu Ser Ala His Ser Met Arg Asn Glu Asn Val Val Pro Thr Val Leu Ala Leu Gly Ser Asp Val Asp Met Asp Val Leu Thr Thr Leu Ser Leu Gly Asp Arg
Ala Ala Val Phe His Glu Lys Asp Tyr Asp Ser Leu Ala Gln Pro Gly Phe Phe Asp Arg Phe Ile Arg Trp Ile Cys
alpha 3
His His His His His His Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser Gly Val Lys Gly Ala Lys Gly Tyr Arg Gly Pro Glu Gly Pro Gln Gly Pro Pro Gly His Gln Gly Pro Pro Gly Pro Asp Glu Cys Glu Ile Leu Asp Ile
Ile Met Lys Met Cys Ser Cys Cys Glu Cys Lys Cys Gly Pro Ile Asp Leu Leu Phe Val Leu Asp Ser Ser Glu Ser Ile Gly Leu Gln Asn Phe Glu Ile Ala Lys Asp Phe Val Val Lys Val Ile Asp Arg Leu Ser Arg Asp Glu
Leu Val Lys Phe Glu Pro Gly Gln Ser Tyr Ala Gly Val Val Gln Tyr Ser His Ser Gln Met Gln Glu His Val Ser Leu Arg Ser Pro Ser Ile Arg Asn Val Gln Glu Leu Lys Glu Ala Ile Lys Ser Leu Gln Trp Met Ala Gly
Gly Thr Phe Thr Gly Glu Ala Leu Gln Tyr Thr Arg Asp Gln Leu Leu Pro Pro Ser Pro Asn Asn Arg Ile Ala Leu Val Ile Thr Asp Gly Arg Ser Asp Thr Gln Arg Asp Thr Thr Pro Leu Asn Val Leu Cys Ser Pro Gly Ile
Gln Val Val Ser Val Gly Ile Lys Asp Val Phe Asp Phe Ile Pro Gly Ser Asp Gln Leu Asn Val Ile Ser Cys Gln Gly Leu Ala Pro Ser Gln Gly Arg Pro Gly Leu Ser Leu Val Lys Glu Asn Tyr Ala Glu Leu Leu Glu Asp
Ala Phe Leu Lys Asn Val Thr Ala Gln Ile Cys Ile Asp Lys Lys Cys Pro Asp Tyr Thr Cys Pro Ile Thr Phe Ser Ser Pro Ala Asp Ile Thr Ile Leu Leu Asp Gly Ser Ala Ser Val Gly Ser His Asn Phe Asp Thr Thr Lys
Arg Phe Ala Lys Arg Leu Ala Glu Arg Phe Leu Thr Ala Gly Arg Thr Asp Pro Ala His Asp Val Arg Val Ala Val Val Gln Tyr Ser Gly Thr Gly Gln Gln Arg Pro Glu Arg Ala Ser Leu Gln Phe Leu Gln Asn Tyr Thr Ala
Leu Ala Ser Ala Val Asp Ala Met Asp Phe Ile Asn Asp Ala Thr Asp Val Asn Asp Ala Leu Gly Tyr Val Thr Arg Phe Tyr Arg Glu Ala Ser Ser Gly Ala Ala Lys Lys Arg Leu Leu Leu Phe Ser Asp Gly Asn Ser Gln Gly
Ala Thr Pro Ala Ala Ile Glu Lys Ala Val Gln Glu Ala Gln Arg Ala Gly Ile Glu Ile Phe Val Val Val Val Gly Arg Gln Val Asn Glu Pro His Ile Arg Val Leu Val Thr Gly Lys Thr Ala Glu Tyr Asp Val Ala Tyr Gly
Glu Ser His Leu Phe Arg Val Pro Ser Tyr Gln Ala Leu Leu Arg Gly Val Phe His Gln Thr Val Ser Arg Lys Val Ala Leu Gly
ヒトのコラーゲンtype IV α1・α2・α3の構造 9gtu（表は50残基ごとに改行）

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