SMTL ID : 2dt5.1 (1 other biounit)

Crystal Structure of TTHA1657 (AT-rich DNA-binding protein) from Thermus thermophilus HB8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: S.30, S.31, R.46, T.57, R.58, G.59, G.61 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.31, A:G.59 Water bridges: A:T.57, A:R.58, A:R.58, A:G.61 Salt bridges: A:R.58 SO4.2: 3 residues within 4Å: Chain A: R.69, R.72, N.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.78 Water bridges: A:R.72 Salt bridges: A:R.69, A:R.72 SO4.3: 5 residues within 4Å: Chain A: Y.98, P.99, G.100, F.101, G.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.101, A:G.102, A:G.102 Water bridges: A:Y.98 SO4.4: 2 residues within 4Å: Chain A: K.155, L.159 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.155 SO4.8: 10 residues within 4Å: Chain B: S.30, S.31, R.46, Y.55, T.57, R.58, G.59, V.60, G.61, Y.62 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.31, B:S.31, B:G.59, B:G.61 Salt bridges: B:R.46 SO4.9: 2 residues within 4Å: Chain B: R.120, P.121 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.120

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

CL.5: 1 residues within 4Å: Chain A: R.195 Ligand excluded by PLIP

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.6: 27 residues within 4Å: Chain A: V.86, G.87, M.88, G.89, R.90, L.91, D.112, V.113, D.114, K.117, V.130, T.147, V.148, P.149, R.150, A.152, F.171, A.172, P.173, V.187, D.188, F.189 Chain B: A.94, L.95, Y.98, P.99, F.189 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.91, A:F.189, B:L.95, B:Y.98, B:Y.98 Hydrogen bonds: A:M.88, A:R.90, A:L.91, A:V.113, A:D.114, A:K.117, A:K.117, A:V.148, A:R.150, A:F.171, A:F.189 Water bridges: A:G.89, A:R.90, A:G.92 Salt bridges: A:R.90, A:R.90 NAD.10: 25 residues within 4Å: Chain A: A.94, L.95, Y.98 Chain B: V.86, G.87, M.88, G.89, R.90, L.91, D.112, V.113, D.114, K.117, V.130, T.147, V.148, P.149, R.150, A.152, F.171, A.172, P.173, V.187, D.188, F.189 21 PLIP interactions: 3 interactions with chain A, 18 interactions with chain B Hydrophobic interactions: A:L.95, A:Y.98, A:Y.98, B:L.91 Hydrogen bonds: B:M.88, B:R.90, B:L.91, B:V.113, B:D.114, B:V.148, B:F.171, B:F.189 Water bridges: B:G.89, B:R.90, B:R.90, B:G.92, B:D.114, B:R.150, B:A.156 Salt bridges: B:R.90, B:R.90

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: G.25, V.26, H.27, R.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.25, A:H.27, A:R.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, A. et al., Crystal structure of TTHA1657 (AT-rich DNA-binding protein; p25) from Thermus thermophilus HB8 at 2.16 A resolution. Proteins (2007)

Release Date

2007-01-02

Peptides

AT-rich DNA-binding protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

AT-rich DNA-binding protein

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