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SMTL ID : 8kdu.1

Crystal structure of trypsin with its substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x I4Q: ethyl (2~{S})-2-benzamido-5-carbamimidamido-pentanoate(Non-covalent)

I4Q.1:

16 residues within 4Å:

Chain A: F.24, H.40, D.171, S.172, C.173, Q.174, G.175, D.176, S.177, S.192, W.193, G.194, G.196, C.197, G.204
Ligands: EOH.11

15 PLIP interactions:

15 interactions with chain A

Hydrophobic interactions: A:W.193
Hydrogen bonds: A:S.172, A:S.172, A:Q.174, A:G.175, A:D.176, A:S.177, A:S.177, A:S.192, A:G.196
Water bridges: A:G.194, A:G.196, A:V.205
Salt bridges: A:H.40, A:D.171

1 x JNR: (2~{R})-2-benzamido-5-carbamimidamido-pentanoic acid(Non-covalent)

JNR.2:

10 residues within 4Å:

Chain A: L.29, N.31, S.32, Q.33, A.94, S.95, L.96, A.101, S.102
Ligands: SO4.5

6 PLIP interactions:

6 interactions with chain A

Hydrophobic interactions: A:L.29, A:L.96
Hydrogen bonds: A:S.32, A:S.32, A:A.94, A:L.96

1 x ARG: ARGININE(Non-covalent)

ARG.3:

2 residues within 4Å:

Chain A: Y.5, K.139

10 PLIP interactions:

4 Ligand-Ligand interactions, 6 interactions with chain A

Hydrogen bonds: R.3, R.3, R.3, R.3, A:K.139
Hydrophobic interactions: A:Y.5, A:Y.5
Water bridges: A:K.139, A:K.139, A:K.139

1 x GAI: GUANIDINE(Non-covalent)

GAI.4:

2 residues within 4Å:

Chain A: Y.5, T.6

4 PLIP interactions:

4 interactions with chain A

Hydrogen bonds: A:T.6, A:T.6, A:T.6, A:T.6

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5:

4 residues within 4Å:

Chain A: N.31, S.32, Q.33
Ligands: JNR.2

4 PLIP interactions:

4 interactions with chain A

Hydrogen bonds: A:S.32, A:S.32, A:Q.33
Water bridges: A:I.30

1 x CA: CALCIUM ION(Non-covalent)

CA.6:

4 residues within 4Å:

Chain A: E.52, N.54, V.57, E.62

6 PLIP interactions:

4 interactions with chain A, 2 Ligand-Water interactions

Metal complexes: A:E.52, A:N.54, A:V.57, A:E.62, H₂O.1, H₂O.5

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.7:	1 residues within 4Å: Chain A: C.109 Ligand excluded by PLIP
CL.8:	1 residues within 4Å: Chain A: G.154 Ligand excluded by PLIP
CL.9:	2 residues within 4Å: Chain A: S.144, D.145 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10:

5 residues within 4Å:

Chain A: N.82, N.83, T.157, S.158, N.159

6 PLIP interactions:

6 interactions with chain A

Hydrogen bonds: A:N.82, A:N.83, A:N.83, A:S.158, A:N.159
Water bridges: A:Y.212

2 x EOH: ETHANOL(Non-functional Binders)

EOH.11:	4 residues within 4Å: Chain A: L.81, Q.155, W.193 Ligands: I4Q.1 No protein-ligand interaction detected (PLIP)
EOH.12:	2 residues within 4Å: Chain A: S.66, K.91 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.91 Hydrogen bonds: A:S.66

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Akbar, Z. et al., Crystal structure of the Michaelis complex of trypsin with N-alpha-benzoyl-l-arginine ethyl ester. J Chin Chem Soc (2024)

Release Date

2024-08-14

Peptides

Cationic trypsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Cationic trypsin

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1aq7.1 | 1auj.1 | 1az8.1 | 1bju.1 | 1bjv.1 | 1c1n.1 | 1c1o.1 | 1c1p.1 | 1c1q.1 | 1c1r.1 | 1c1s.1 | 1c1t.1 | 1c2d.1 | 1c2e.1 | 1c2f.1 | 1c2g.1 | 1c2h.1 | 1c2i.1 | 1c2j.1 | 1c2k.1 | 1c2l.1 | 1c2m.1 | 1c5p.1 | 1c5q.1 | 1c5r.1 | 1c5s.1 | 1c5t.1 | 1c5u.1 | 1c5v.1 | 1c9t.1 more...less...

1c9t.2 | 1c9t.3 | 1c9t.4 | 1c9t.5 | 1c9t.6 | 1ce5.1 | 1d6r.1 | 1eb2.1 | 1ejm.1 | 1ejm.2 | 1ejm.3 | 1f2s.1 | 1g36.1 | 1g9i.1 | 1gbt.1 | 1ghz.1 | 1gi0.1 | 1gi1.1 | 1gi2.1 | 1gi3.1 | 1gi4.1 | 1gi5.1 | 1gi6.1 | 1gj6.1 | 1j8a.1 | 1jir.1 | 1jrs.1 | 1jrt.1 | 1k1i.1 | 1k1j.1 | 1k1l.1 | 1k1m.1 | 1k1n.1 | 1k1o.1 | 1k1p.1 | 1max.1 | 1may.1 | 1mts.1 | 1mtu.1 | 1mtv.1 | 1mtw.1 | 1n6x.1 | 1n6y.1 | 1nc6.1 | 1o2h.1 | 1o2i.1 | 1o2j.1 | 1o2k.1 | 1o2l.1 | 1o2m.1 | 1o2n.1 | 1o2o.1 | 1o2p.1 | 1o2q.1 | 1o2r.1 | 1o2s.1 | 1o2t.1 | 1o2u.1 | 1o2v.1 | 1o2w.1 | 1o2x.1 | 1o2y.1 | 1o2z.1 | 1o30.1 | 1o31.1 | 1o32.1 | 1o33.1 | 1o34.1 | 1o35.1 | 1o36.1 | 1o37.1 | 1o38.1 | 1o39.1 | 1o3a.1 | 1o3b.1 | 1o3c.1 | 1o3d.1 | 1o3e.1 | 1o3f.1 | 1o3g.1 | 1o3h.1 | 1o3i.1 | 1o3j.1 | 1o3k.1 | 1o3l.1 | 1o3m.1 | 1o3n.1 | 1o3o.1 | 1ox1.1 | 1oyq.1 | 1p2i.1 | 1p2j.1 | 1p2j.2 | 1p2j.3 | 1p2k.1 | 1ppc.1 | 1ppe.1 | 1pph.1 | 1qa0.1 | 1qb1.1 | 1qb6.1 | 1qb9.1 | 1qbn.1 | 1qbo.1 | 1qcp.1 | 1ql7.1 | 1ql8.1 | 1rxp.1 | 1s0q.1 | 1s0r.1 | 1sbw.1 | 1sfi.1 | 1smf.1 | 1tab.1 | 1tio.1 | 1tld.1 | 1tpa.1 | 1tpa.2 | 1tpo.1 | 1tpp.1 | 1tps.1 | 1tx7.1 | 1tx8.1 | 1tyn.1 | 1xuf.1 | 1xug.1 | 1xuh.1 | 1xui.1 | 1xuj.1 | 1xuk.1 | 1y3u.1 | 1y3v.1 | 1y3w.1 | 1y3x.1 | 1y3y.1 | 1yp9.1 | 1yyy.1 | 2a7h.1 | 2age.1 | 2agg.1 | 2agi.1 | 2ah4.1 | 2ayw.1 | 2blv.1 | 2blw.1 | 2btc.1 | 2bza.1 | 2cmy.1 | 2d8w.1 | 2f3c.1 | 2fi3.1 | 2fi3.2 | 2fi3.3 | 2fi3.4 | 2fi3.5 | 2fi3.6 | 2fi3.7 | 2fx4.1 | 2fx6.1 | 2g55.1 | 2g5n.1 | 2g5v.1 | 2g81.1 | 2g8t.1 | 2iln.1 | 2j9n.1 | 2o9q.1 | 2otv.1 | 2oxs.1 | 2plx.1 | 2ptc.1 | 2ptc.2 | 2ptn.1 | 2qn5.1 | 2qyi.1 | 2tio.1 | 2uuy.1 | 2xtt.1 | 2zdk.1 | 2zdl.1 | 2zdm.1 | 2zdn.1 | 2zfs.1 | 2zft.1 | 2zhd.1 | 2zq1.1 | 2zq2.1 | 3a7t.1 | 3a7v.1 | 3a7w.1 | 3a7x.1 | 3a7y.1 | 3a7z.1 | 3a80.1 | 3a81.1 | 3a82.1 | 3a83.1 | 3a84.1 | 3a85.1 | 3a86.1 | 3a87.1 | 3a88.1 | 3a89.1 | 3a8a.1 | 3a8b.1 | 3a8c.1 | 3a8d.1 | 3aas.1 | 3aau.1 | 3aav.1 | 3aav.2 | 3ati.1 | 3atk.1 | 3atl.1 | 3atm.1 | 3btd.1 | 3btd.2 | 3bte.1 | 3bte.2 | 3btf.1 | 3btf.2 | 3btf.3 | 3btg.1 | 3btg.2 | 3btg.3 | 3bth.1 | 3bth.2 | 3bth.3 | 3btk.1 | 3btk.2 | 3btk.3 | 3btm.1 | 3btm.2 | 3btm.3 | 3btq.1 | 3btq.2 | 3btq.3 | 3btt.1 | 3btt.2 | 3btt.3 | 3btw.1 | 3btw.2 | 3btw.3 | 3d65.1 | 3e8l.1 | 3gy2.1 | 3gy3.1 | 3gy4.1 | 3gy5.1 | 3gy6.1 | 3gy7.1 | 3gy8.1 | 3i29.1 | 3iti.1 | 3ljj.1 | 3ljo.1 | 3m35.1 | 3m7q.1 | 3mfj.1 | 3mi4.1 | 3nk8.1 | 3nkk.1 | 3otj.1 | 3ptb.1 | 3ptn.1 | 3rdz.1 | 3rdz.2 | 3ru4.1 | 3rxa.1 | 3rxb.1 | 3rxc.1 | 3rxd.1 | 3rxe.1 | 3rxf.1 | 3rxg.1 | 3rxh.1 | 3rxi.1 | 3rxj.1 | 3rxk.1 | 3rxl.1 | 3rxm.1 | 3rxo.1 | 3rxp.1 | 3rxq.1 | 3rxr.1 | 3rxs.1 | 3rxt.1 | 3rxu.1 | 3rxv.1 | 3t25.1 | 3t26.1 | 3t27.1 | 3t28.1 | 3t29.1 | 3vpk.1 | 4ab8.1 | 4ab9.1 | 4aba.1 | 4abb.1 | 4abd.1 | 4abe.1 | 4abf.1 | 4abg.1 | 4abh.1 | 4abi.1 | 4abj.1 | 4aoq.1 | 4aoq.2 | 4aoq.3 | 4aor.1 | 4aor.2 | 4aor.3 | 4hgc.1 | 4i8g.1 | 4i8h.1 | 4i8j.1 | 4i8k.1 | 4i8l.1 | 4j2y.1 | 4kts.1 | 4ktu.1 | 4mtb.1 | 4ncy.1 | 4tpy.1 | 4u2w.1 | 4y0y.1 | 4y0z.1 | 4y10.1 | 4y11.1 | 4yta.1 | 5eg4.1 | 5f6m.1 | 5gib.1 | 5gib.2 | 5gxp.1 | 5k7r.1 | 5lgo.1 | 5lh4.1 | 5lh8.1 | 5mn1.1 | 5mna.1 | 5mnb.1 | 5mnc.1 | 5mne.1 | 5mnf.1 | 5mng.1 | 5mnh.1 | 5mnk.1 | 5mnl.1 | 5mnm.1 | 5mnn.1 | 5mno.1 | 5mnp.1 | 5mnq.1 | 5mnx.1 | 5mny.1 | 5mnz.1 | 5mo0.1 | 5mo1.1 | 5mo2.1 | 5mon.1 | 5moo.1 | 5mop.1 | 5moq.1 | 5mor.1 | 5mos.1 | 5ptp.1 | 5t3h.1 | 6avl.1 | 6b6n.1 | 6b6o.1 | 6b6p.1 | 6b6q.1 | 6b6r.1 | 6b6s.1 | 6b6t.1 | 6bfp.1 | 6bvh.1 | 6dwf.1 | 6dwf.2 | 6dwf.3 | 6dwf.4 | 6dwf.5 | 6dwf.6 | 6dwh.1 | 6dwh.2 | 6dwh.3 | 6dwu.1 | 6dwu.2 | 6dwu.3 | 6dwu.4 | 6dwu.5 | 6dwu.6 | 6dwu.7 | 6dwu.8 | 6dwu.9 | 6dwu.10 | 6dwu.11 | 6dwu.12 | 6dwu.13 | 6dwu.14 | 6dwu.15 | 6dwu.16 | 6dwu.17 | 6dwu.18 | 6dwu.19 | 6dwu.20 | 6dwu.21 | 6dwu.22 | 6dwu.23 | 6dwu.24 | 6dwu.25 | 6dwu.26 | 6dwu.27 | 6dwu.28 | 6dwu.29 | 6dwu.30 | 6dwu.31 | 6dwu.32 | 6dwu.33 | 6dwu.34 | 6dwu.35 | 6dwu.36 | 6dwu.37 | 6dwu.38 | 6dwu.39 | 6dwu.40 | 6dwu.41 | 6dwu.42 | 6dwu.43 | 6dwu.44 | 6dzf.1 | 6e5m.1 | 6eat.1 | 6eau.1 | 6eav.1 | 6eaw.1 | 6eax.1 | 6fid.1 | 6qih.1 | 6sux.1 | 6sv0.1 | 6sv6.1 | 6sv8.1 | 6sv9.1 | 6svb.1 | 6svd.1 | 6svg.1 | 6svi.1 | 6svj.1 | 6svn.1 | 6svr.1 | 6svu.1 | 6svv.1 | 6svw.1 | 6svx.1 | 6svz.1 | 6sw0.1 | 6u22.1 | 6vxy.1 | 6xyg.1 | 6xyk.1 | 6yit.1 | 6yiu.1 | 6yiv.1 | 6yiw.1 | 6yix.1 | 6yiy.1 | 6yza.1 | 6yzc.1 | 6zfj.1 | 6zfk.1 | 6zq2.1 | 7al8.1 | 7ays.1 | 7brv.1 | 7brw.1 | 7brx.1 | 7bry.1 | 7brz.1 | 7bs0.1 | 7bs1.1 | 7bs2.1 | 7bs3.1 | 7bs4.1 | 7bs5.1 | 7bs6.1 | 7bs7.1 | 7bs8.1 | 7bs9.1 | 7bsa.1 | 7jr1.1 | 7jr1.2 | 7jr1.3 | 7jr1.4 | 7jr1.5 | 7jr1.6 | 7jr2.1 | 7jr2.2 | 7jr2.3 | 7jr2.4 | 7jr2.5 | 7jr2.6 | 7jwx.1 | 7jwx.2 | 7jwx.3 | 7jwx.4 | 7ph1.1 | 7q0w.1 | 7q0x.1 | 7vo7.1 | 7wa0.1 | 7wa2.1 | 7wb6.1 | 7wb7.1 | 7wb8.1 | 7wb9.1 | 7wba.1 | 7z25.1 | 7z2i.1 | 8iyv.1 | 8izh.1 | 8izi.1 | 8izk.1 | 8uo7.1 | 8utl.1 | 8wk1.1 | 9bok.1 | 9bom.1

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Background

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