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SMTL ID : 6y9h.1

Thrombin in complex with D-Phe-Pro-m-Trifluoromethylbenzylamide derivative (phe2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x DPN- PRO- OGZ: D-Phe-Pro-m-Trifluoromethylbenzylamide derivative (phe2)(Non-covalent)

DPN-PRO-OGZ.1:

20 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, E.229, G.230, G.238, F.239

11 PLIP interactions:

11 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:I.179, B:V.225, B:W.227
Hydrogen bonds: B:S.226, B:G.228, B:G.228
Water bridges: B:E.202
Halogen bonds: B:F.239

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

NA.2:	4 residues within 4Å: Chain B: K.174, D.175, T.177, R.178 No protein-ligand interaction detected (PLIP)
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 DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4:

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

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

PO4.5:	7 residues within 4Å: Chain B: R.89, N.91, N.95, D.97, R.98, R.180, T.182 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.89, B:N.91, B:D.97, B:D.97, B:D.97 Water bridges: B:E.94, B:R.98, B:R.180, B:R.180, B:R.180 Salt bridges: B:R.98, B:R.180
PO4.7:	4 residues within 4Å: Chain B: E.124, T.125, S.128, F.215 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.128

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

NAG.6:

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Sandner, A. et al., Thrombin in complex with D-Phe-Pro-m-Trifluoromethylbenzylamide derivative (phe2). To be published

Release Date

2021-03-31

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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