SMTL ID : 2i6t.1 (1 other biounit)

Orthorhombic Structure of the LDH domain of Human Ubiquitin-conjugating Enzyme E2-like Isoform A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: A.168, Q.169, T.170, S.171, E.194 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.168, A:T.170, A:S.171 Water bridges: A:Q.169, A:Q.169, A:T.170, A:S.171, A:E.194 SO4.2: 4 residues within 4Å: Chain A: V.196, S.197, S.200 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.197, A:S.197, A:S.200 SO4.8: 5 residues within 4Å: Chain B: A.168, Q.169, T.170, S.171, E.194 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.170, B:S.171, B:S.171, B:E.194 SO4.9: 4 residues within 4Å: Chain B: V.196, S.197, S.200 Ligands: GOL.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.197, B:S.197, B:S.200 Water bridges: B:S.197, B:S.197, B:S.200 SO4.12: 5 residues within 4Å: Chain C: A.168, Q.169, T.170, S.171, E.194 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:A.168, C:T.170, C:S.171 Water bridges: C:Q.169, C:Q.169, C:T.170, C:S.171, C:E.194 SO4.13: 4 residues within 4Å: Chain C: V.196, S.197, S.200 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.197, C:S.197, C:S.200 SO4.19: 5 residues within 4Å: Chain D: A.168, Q.169, T.170, S.171, E.194 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.170, D:S.171, D:S.171, D:E.194 SO4.20: 4 residues within 4Å: Chain D: V.196, S.197, S.200 Ligands: GOL.22 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.197, D:S.197, D:S.200 Water bridges: D:S.197, D:S.197, D:S.200

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: I.149, G.150, C.151, N.152, L.153, D.154, Q.181, Q.217, S.225 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.149, A:N.152, A:L.153, A:D.154, A:D.154, A:Q.217, A:S.225 Water bridges: A:Q.181 GOL.4: 4 residues within 4Å: Chain A: T.199, S.200, Q.203 Ligands: SO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.199, A:T.199, A:T.199, A:Q.203 Water bridges: A:S.200, A:S.200 GOL.5: 4 residues within 4Å: Chain A: K.70, D.71, L.72, S.73 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.70, A:L.72, A:S.73 Water bridges: A:D.71, A:S.73 GOL.6: 9 residues within 4Å: Chain A: D.57, I.60, F.61 Chain B: N.152, L.153, Q.156, R.157, L.224, S.225 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.152, B:S.225, A:D.57 GOL.7: 7 residues within 4Å: Chain A: Y.250, Y.251, P.262, V.273, I.274, K.275, T.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.276, A:T.276 GOL.10: 9 residues within 4Å: Chain B: I.149, G.150, C.151, N.152, L.153, D.154, Q.181, Q.217, S.225 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.152, B:L.153, B:D.154, B:D.154, B:Q.217, B:S.225, B:S.225 GOL.11: 4 residues within 4Å: Chain B: T.199, S.200, Q.203 Ligands: SO4.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.199, B:T.199, B:T.199, B:Q.203 Water bridges: B:S.200, B:S.200 GOL.14: 9 residues within 4Å: Chain C: I.149, G.150, C.151, N.152, L.153, D.154, Q.181, Q.217, S.225 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:I.149, C:N.152, C:L.153, C:D.154, C:D.154, C:Q.217, C:S.225 Water bridges: C:Q.181 GOL.15: 4 residues within 4Å: Chain C: T.199, S.200, Q.203 Ligands: SO4.13 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.199, C:T.199, C:T.199, C:Q.203 Water bridges: C:S.200, C:S.200 GOL.16: 4 residues within 4Å: Chain C: K.70, D.71, L.72, S.73 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.70, C:L.72, C:S.73 Water bridges: C:D.71, C:S.73 GOL.17: 9 residues within 4Å: Chain C: D.57, I.60, F.61 Chain D: N.152, L.153, Q.156, R.157, L.224, S.225 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.152, D:S.225, C:D.57 GOL.18: 7 residues within 4Å: Chain C: Y.250, Y.251, P.262, V.273, I.274, K.275, T.276 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.276, C:T.276 GOL.21: 9 residues within 4Å: Chain D: I.149, G.150, C.151, N.152, L.153, D.154, Q.181, Q.217, S.225 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.152, D:L.153, D:D.154, D:D.154, D:Q.217, D:S.225, D:S.225 GOL.22: 4 residues within 4Å: Chain D: T.199, S.200, Q.203 Ligands: SO4.20 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.199, D:T.199, D:T.199, D:Q.203 Water bridges: D:S.200, D:S.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Avvakumov, G.V. et al., Structural Investigation into the L-lactate Dehydrogenase Domain of Human Ubiquitin-conjugating Enzyme E2-like Isoform A. To be Published

Release Date

2006-10-24

Peptides

UBIQUITIN-CONJUGATING ENZYME E2-LIKE ISOFORM A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

UBIQUITIN-CONJUGATING ENZYME E2-LIKE ISOFORM A

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