SMTL ID : 3geg.1

Fingerprint and Structural Analysis of a SCOR enzyme with its bound cofactor from Clostridium thermocellum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: G.9, H.12, G.13, I.14, D.33, I.34, D.35, R.38, G.54, D.55, V.56, N.82, A.83, C.84, R.85, Y.101, V.105, I.131, A.132, S.133, Y.146, K.150, P.175, G.176, W.177, I.178, V.180 Ligands: GOL.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.175 Hydrogen bonds: A:I.14, A:I.34, A:D.35, A:R.38, A:D.55, A:V.56, A:N.82, A:R.85, A:Y.101, A:K.150, A:I.178, A:I.178 Water bridges: A:N.82 Salt bridges: A:H.12, A:R.85 NAD.5: 27 residues within 4Å: Chain B: G.9, H.12, G.13, I.14, D.33, I.34, D.35, G.54, D.55, V.56, N.82, A.83, C.84, R.85, Y.101, V.105, I.131, A.132, S.133, Y.146, K.150, P.175, G.176, W.177, I.178, V.180 Ligands: GOL.6 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:I.14, B:I.34, B:D.35, B:D.55, B:D.55, B:V.56, B:N.82, B:Y.146, B:K.150, B:I.178, B:I.178 Water bridges: B:G.15, B:N.82, B:C.84 Salt bridges: B:H.12, B:R.85 NAD.8: 28 residues within 4Å: Chain C: G.9, H.12, G.13, I.14, D.33, I.34, D.35, R.38, G.54, D.55, V.56, N.82, A.83, C.84, R.85, Y.101, V.105, I.131, A.132, S.133, Y.146, K.150, P.175, G.176, W.177, I.178, V.180 Ligands: GOL.9 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:P.175 Hydrogen bonds: C:I.14, C:I.34, C:D.35, C:R.38, C:D.55, C:V.56, C:N.82, C:R.85, C:Y.101, C:K.150, C:I.178, C:I.178 Water bridges: C:N.82 Salt bridges: C:H.12, C:R.85 NAD.12: 27 residues within 4Å: Chain D: G.9, H.12, G.13, I.14, D.33, I.34, D.35, G.54, D.55, V.56, N.82, A.83, C.84, R.85, Y.101, V.105, I.131, A.132, S.133, Y.146, K.150, P.175, G.176, W.177, I.178, V.180 Ligands: GOL.13 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:I.14, D:I.34, D:D.35, D:D.55, D:D.55, D:V.56, D:N.82, D:Y.146, D:K.150, D:I.178, D:I.178 Water bridges: D:G.15, D:N.82, D:C.84 Salt bridges: D:H.12, D:R.85

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.135 Chain D: Y.235, D.238 Ligands: NAD.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.135, D:D.238 Water bridges: A:S.133, A:R.135 GOL.6: 5 residues within 4Å: Chain B: R.135, W.177 Chain C: Y.235, D.238 Ligands: NAD.5 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.135, C:D.238 Water bridges: B:S.133, B:R.135, B:R.135, C:D.238 GOL.9: 4 residues within 4Å: Chain B: Y.235, D.238 Chain C: R.135 Ligands: NAD.8 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.135, B:D.238 Water bridges: C:S.133, C:R.135 GOL.13: 5 residues within 4Å: Chain A: Y.235, D.238 Chain D: R.135, W.177 Ligands: NAD.12 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.135, A:D.238 Water bridges: D:S.133, D:R.135, D:R.135, A:D.238

2 x THJ: THIOSULFATE(Non-covalent)

THJ.3: 4 residues within 4Å: Chain A: K.16, D.41, F.42, R.46 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.16, A:R.46 THJ.10: 4 residues within 4Å: Chain C: K.16, D.41, F.42, R.46 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.16, C:R.46

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

NA.4: 3 residues within 4Å: Chain A: A.43, R.46, L.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.43 Water bridges: A:E.45 NA.7: 3 residues within 4Å: Chain B: A.43, R.46, L.49 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.46, B:L.49 Water bridges: B:E.45 NA.11: 3 residues within 4Å: Chain C: A.43, R.46, L.49 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.43 Water bridges: C:E.45 NA.14: 3 residues within 4Å: Chain D: A.43, R.46, L.49 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.46, D:R.46 Water bridges: D:E.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huether, R. et al., Sequence fingerprint and structural analysis of the SCOR enzyme A3DFK9 from Clostridium thermocellum. Proteins (2010)

Release Date

2009-03-17

Peptides

Short-chain dehydrogenase/reductase SDR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Short-chain dehydrogenase/reductase SDR

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