SMTL ID : 1s9r.1

CRYSTAL STRUCTURE OF ARGININE DEIMINASE COVALENTLY LINKED WITH A REACTION INTERMEDIATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x ARG: ARGININE(Covalent)

ARG.1: 14 residues within 4Å: Chain A: L.44, N.155, F.158, R.160, D.161, R.180, G.215, R.232, M.268, H.269, D.271, G.392, M.393, C.398 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.158 Hydrogen bonds: A:L.44, A:N.155, A:D.161, A:D.161, R.1 Salt bridges: A:R.180, A:R.232 ARG.7: 15 residues within 4Å: Chain B: L.44, N.155, F.158, R.160, D.161, R.180, G.215, R.232, M.268, H.269, D.271, G.392, M.393, G.394, C.398 9 PLIP interactions: 8 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.158 Hydrogen bonds: B:L.44, B:N.155, B:D.161, B:D.161, B:H.269, R.7 Salt bridges: B:R.180, B:R.232

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 8 residues within 4Å: Chain A: R.344, E.345, F.348, R.366, N.367 Chain B: I.48, L.49, E.50 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:L.49, A:R.344, A:R.366, A:R.366 Water bridges: B:S.51, A:R.344 TRS.8: 8 residues within 4Å: Chain A: I.48, L.49, E.50 Chain B: R.344, E.345, F.348, R.366, N.367 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.344, B:R.366, B:R.366, A:L.49 Water bridges: B:E.345, B:E.345, A:S.51

9 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 9 residues within 4Å: Chain A: N.387 Ligands: UNX.4, UNX.5, UNX.6, UNX.9, UNX.10, UNX.11, UNX.12, UNX.13 No protein-ligand interaction detected (PLIP) UNX.4: 8 residues within 4Å: Ligands: UNX.3, UNX.5, UNX.6, UNX.9, UNX.10, UNX.11, UNX.12, UNX.13 No protein-ligand interaction detected (PLIP) UNX.5: 6 residues within 4Å: Ligands: UNX.3, UNX.4, UNX.10, UNX.11, UNX.12, UNX.13 No protein-ligand interaction detected (PLIP) UNX.6: 10 residues within 4Å: Chain A: E.57, N.387, Q.388 Chain B: Q.388 Ligands: UNX.3, UNX.4, UNX.9, UNX.10, UNX.11, UNX.13 No protein-ligand interaction detected (PLIP) UNX.9: 10 residues within 4Å: Chain A: Q.388 Chain B: E.57, N.387, Q.388 Ligands: UNX.3, UNX.4, UNX.6, UNX.10, UNX.11, UNX.13 No protein-ligand interaction detected (PLIP) UNX.10: 11 residues within 4Å: Chain A: N.387, Q.388 Chain B: Q.388 Ligands: UNX.3, UNX.4, UNX.5, UNX.6, UNX.9, UNX.11, UNX.12, UNX.13 No protein-ligand interaction detected (PLIP) UNX.11: 8 residues within 4Å: Ligands: UNX.3, UNX.4, UNX.5, UNX.6, UNX.9, UNX.10, UNX.12, UNX.13 No protein-ligand interaction detected (PLIP) UNX.12: 6 residues within 4Å: Ligands: UNX.3, UNX.4, UNX.5, UNX.10, UNX.11, UNX.13 No protein-ligand interaction detected (PLIP) UNX.13: 9 residues within 4Å: Chain B: N.387 Ligands: UNX.3, UNX.4, UNX.5, UNX.6, UNX.9, UNX.10, UNX.11, UNX.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Das, K. et al., Crystal Structures of Arginine Deiminase with Covalent Reaction Intermediates: Implications for Catalytic Mechanism. Structure (2004)

Release Date

2004-04-13

Peptides

Arginine deiminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Arginine deiminase