SMTL ID : 1z2u.1

The 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: P.60, T.61, D.62, K.66 Ligands: UNX.11 Ligand excluded by PLIP CL.2: 1 residues within 4Å: Chain A: K.147 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: R.134, N.138 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: Q.14, R.18 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: G.1, S.2, H.3, K.7 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Ligands: BU3.8 Ligand excluded by PLIP

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

NA.7: 3 residues within 4Å: Chain A: D.115, P.116, Y.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.116, A:Y.130

2 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.8: 2 residues within 4Å: Chain A: Y.148 Ligands: CL.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.148 BU3.9: 1 residues within 4Å: Chain A: R.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.18 Water bridges: A:R.18

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

UNX.10: 2 residues within 4Å: Chain A: N.138, R.142 No protein-ligand interaction detected (PLIP) UNX.11: 1 residues within 4Å: Ligands: CL.1 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain A: D.133, R.136 No protein-ligand interaction detected (PLIP) UNX.13: 1 residues within 4Å: Chain A: S.25 No protein-ligand interaction detected (PLIP) UNX.14: 3 residues within 4Å: Chain A: L.89, D.90, N.117 No protein-ligand interaction detected (PLIP) UNX.15: 4 residues within 4Å: Chain A: V.29, D.32 Ligands: UNX.17, UNX.18 No protein-ligand interaction detected (PLIP) UNX.16: 4 residues within 4Å: Chain A: S.25, Q.37, A.38, T.39 No protein-ligand interaction detected (PLIP) UNX.17: 3 residues within 4Å: Chain A: G.30, D.31 Ligands: UNX.15 No protein-ligand interaction detected (PLIP) UNX.18: 4 residues within 4Å: Chain A: V.29, H.35 Ligands: UNX.15, UNX.19 No protein-ligand interaction detected (PLIP) UNX.19: 2 residues within 4Å: Chain A: D.32 Ligands: UNX.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gavira, J.A. et al., The 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance. To be published

Release Date

2005-03-22

Peptides

Ubiquitin-conjugating enzyme E2 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ubiquitin-conjugating enzyme E2 2