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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-tetramer

Ligands

12 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: 4 residues within 4Å: Chain A: K.155, L.159 Chain C: D.131 Ligands: SO4.14 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Salt bridges: A:K.155, C:K.155 Water bridges: C:D.131 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: 3 residues within 4Å: Chain B: R.120, P.121 Chain D: R.123 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Water bridges: D:F.101, D:G.102, D:R.123, D:R.123 Salt bridges: D:R.123, B:R.120 SO4.11: 7 residues within 4Å: Chain C: S.30, S.31, R.46, T.57, R.58, G.59, G.61 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.31, C:G.59 Water bridges: C:T.57, C:R.58, C:R.58, C:G.61 Salt bridges: C:R.58 SO4.12: 3 residues within 4Å: Chain C: R.69, R.72, N.78 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.78 Water bridges: C:R.72 Salt bridges: C:R.69, C:R.72 SO4.13: 5 residues within 4Å: Chain C: Y.98, P.99, G.100, F.101, G.102 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.101, C:G.102, C:G.102 Water bridges: C:Y.98 SO4.14: 4 residues within 4Å: Chain A: D.131 Chain C: K.155, L.159 Ligands: SO4.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:K.155, C:K.155 SO4.18: 10 residues within 4Å: Chain D: S.30, S.31, R.46, Y.55, T.57, R.58, G.59, V.60, G.61, Y.62 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.31, D:S.31, D:Y.55, D:G.59, D:G.61 Salt bridges: D:R.46 SO4.19: 3 residues within 4Å: Chain B: R.123 Chain D: R.120, P.121 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Water bridges: B:F.101, B:G.102, B:R.123, B:R.123 Salt bridges: B:R.123, D:R.120

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

CL.5: 1 residues within 4Å: Chain A: R.195 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain C: R.195 Ligand excluded by PLIP

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

NAD.6: 28 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 Chain C: E.151 22 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B, 1 interactions with chain C 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, C:E.151 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 NAD.16: 28 residues within 4Å: Chain A: E.151 Chain C: 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 D: A.94, L.95, Y.98, P.99, F.189 23 PLIP interactions: 18 interactions with chain C, 4 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: C:L.91, C:F.189, D:L.95, D:Y.98, D:Y.98 Hydrogen bonds: C:M.88, C:R.90, C:L.91, C:V.113, C:D.114, C:K.117, C:K.117, C:V.148, C:R.150, C:F.171, C:F.189 Water bridges: C:G.89, C:R.90, C:G.92, D:Y.98, A:E.151 Salt bridges: C:R.90, C:R.90 NAD.20: 25 residues within 4Å: Chain C: A.94, L.95, Y.98 Chain D: 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 22 PLIP interactions: 19 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.91, C:L.95, C:Y.98, C:Y.98 Hydrogen bonds: D:M.88, D:R.90, D:L.91, D:V.113, D:D.114, D:V.148, D:F.171, D:F.189 Water bridges: D:G.89, D:R.90, D:R.90, D:G.92, D:D.114, D:D.114, D:R.150, D:A.156 Salt bridges: D:R.90, D:R.90

2 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 GOL.17: 4 residues within 4Å: Chain C: G.25, V.26, H.27, R.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.25, C:H.27, C: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

AT-rich DNA-binding protein

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