SMTL ID : 3h0n.1

Crystal structure of a duf1470 family protein (jann_2411) from jannaschia sp. ccs1 at 1.45 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.148, C.153, C.169, C.173 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.148, A:C.153, A:C.169, A:C.173 ZN.10: 4 residues within 4Å: Chain B: C.148, C.153, C.169, C.173 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.148, B:C.153, B:C.169, B:C.173

2 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 4 residues within 4Å: Chain A: H.113, H.115, M.124 Ligands: ACT.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.113, A:H.115, H2O.5, H2O.10 NI.11: 4 residues within 4Å: Chain B: H.113, H.115, M.124 Ligands: ACT.16 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.113, B:H.115, H2O.14, H2O.19

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

NA.3: 4 residues within 4Å: Chain A: C.148, N.149, A.150, C.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.149, A:C.153 NA.4: 4 residues within 4Å: Chain A: L.93, R.94, H.96 Chain B: T.99 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.96, A:A.98, B:T.99 NA.12: 4 residues within 4Å: Chain B: C.148, N.149, A.150, C.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.148, B:C.153 NA.13: 4 residues within 4Å: Chain A: T.99 Chain B: L.93, R.94, H.96 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.99, B:A.98

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: E.8, R.111 Chain B: G.138, H.139, Q.140 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.8, A:R.111, A:R.111, B:H.139 Water bridges: A:Y.7 GOL.6: 6 residues within 4Å: Chain A: N.20, R.27, R.28, R.155, C.169, S.170 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.28, A:C.169, A:S.170 Water bridges: A:N.20, A:R.27, A:R.27, A:R.27 GOL.14: 5 residues within 4Å: Chain A: G.138, H.139, Q.140 Chain B: E.8, R.111 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:H.139, B:E.8, B:R.111, B:R.111 Water bridges: B:Y.7 GOL.15: 6 residues within 4Å: Chain B: N.20, R.27, R.28, R.155, C.169, S.170 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.28, B:C.169, B:S.170 Water bridges: B:N.20, B:R.27, B:R.27, B:R.27

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 8 residues within 4Å: Chain A: Y.7, T.10, L.112, H.113, H.114, H.115, I.128 Ligands: NI.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.7, A:T.10, A:I.128 Hydrogen bonds: A:H.114 Salt bridges: A:H.114 ACT.8: 1 residues within 4Å: Chain A: V.142 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.140, A:R.143 Salt bridges: A:R.143 ACT.9: 4 residues within 4Å: Chain A: P.97, A.98, T.99, P.116 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.116 Hydrogen bonds: A:A.98, A:T.99, A:T.99 ACT.16: 8 residues within 4Å: Chain B: Y.7, T.10, L.112, H.113, H.114, H.115, I.128 Ligands: NI.11 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.7, B:T.10, B:I.128 Hydrogen bonds: B:H.114, B:H.115 Salt bridges: B:H.114 ACT.17: 1 residues within 4Å: Chain B: V.142 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.140, B:R.143 Salt bridges: B:R.143 ACT.18: 4 residues within 4Å: Chain B: P.97, A.98, T.99, P.116 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.116 Hydrogen bonds: B:A.98, B:T.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bakolitsa, C. et al., The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45  resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator. Acta Crystallogr.,Sect.F (2010)

Release Date

2009-04-21

Peptides

uncharacterized protein DUF1470: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

uncharacterized protein DUF1470