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SMTL ID : 6yn3.1

Thrombin in complex with 4-hydroxybenzamide (j89)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1:

6 residues within 4Å:

Chain B: R.89, N.91, D.97, R.98, R.180, T.182

7 PLIP interactions:

7 interactions with chain B

Hydrogen bonds: B:N.91, B:D.97, B:D.97
Water bridges: B:R.180, B:R.180
Salt bridges: B:R.98, B:R.180

2 x NA: SODIUM ION(Non-functional Binders)

NA.2:	4 residues within 4Å: Chain B: K.174, D.175, T.177, R.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.177
NA.3:	5 residues within 4Å: Chain B: D.232, R.233, D.234, G.235, K.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.235, B:G.238

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4:

4 residues within 4Å:

Chain B: L.46, P.48, N.53, W.92

3 PLIP interactions:

3 interactions with chain B

Hydrophobic interactions: B:L.46, B:P.48
Hydrogen bonds: B:N.53

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5:	4 residues within 4Å: Chain B: E.124, T.125, S.128, F.215 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.215
DMS.6:	7 residues within 4Å: Chain B: L.130, Q.131, A.132, I.167, V.168, R.170, F.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.170

1 x HBD: 4-HYDROXYBENZAMIDE(Non-covalent)

HBD.7:

11 residues within 4Å:

Chain B: D.199, A.200, C.201, E.202, S.205, V.225, W.227, G.228, G.230, G.238, F.239

11 PLIP interactions:

11 interactions with chain B

Hydrophobic interactions: B:A.200, B:V.225
Hydrogen bonds: B:E.202, B:E.202, B:S.205
Water bridges: B:D.199, B:G.203, B:D.204, B:G.228, B:E.229, B:G.238

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Scanlan, W. et al., Thrombin in complex with 4-hydroxybenzamide (j89). To be published

Release Date

2021-04-21

Peptides

Prothrombin: A
Prothrombin: B
Hirudin variant-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Prothrombin

Prothrombin

Hirudin variant-2

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1a2c.1 | 1a3b.1 | 1a3e.1 | 1a46.1 | 1a4w.1 | 1a5g.1 | 1a61.1 | 1abi.1 | 1abj.1 | 1ad8.1 | 1ae8.1 | 1afe.1 | 1aht.1 | 1ai8.1 | 1aix.1 | 1awf.1 | 1awh.1 | 1awh.2 | 1ay6.1 | 1b5g.1 | 1b7x.1 | 1ba8.1 | 1bb0.1 | 1bcu.1 | 1bmm.1 | 1bmn.1 | 1bth.1 | 1bth.2 | 1c1u.1 | 1c1v.1 more...less...

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