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PDB ID Mentions in PubMed Central Article count: 7

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Improved prediction of critical residues for protein function based on network and phylogenetic analyses.

(2005) BMC Bioinformatics 6

PubMed: 16124876 | PubMedCentral: PMC1208857 | DOI: 10.1186/1471-2105-6-213

The 128 PDB names used in this set are: 1a3c, 1a6q, 1a7j, 1aac, 1ac5, 1ah7, 1ak1, 1ako, 1amj, 1an8, 1apq, 1arv, 1atg, 1auz, 1ayl, 1ayx, 1az9, 1b64, 1bag, 1bdb, 1bea, 1bfd, 1bia, 1bif, 1bix, 1bk0, 1bli... 1bn5, 1bor, 1boy, 1bp1, 1bqk, 1brt, 1btl, 1c25, 1ca1, 1cby, 1cex, 1cfb, 1chc, 1chd, 1csh, 1ctn, 1ctt, 1cvl, 1dmr, 1drw, 1dxy, 1ecl, 1eh2, 1emn, 1esl, 1eut, 1far, 1fnc, 1gca, 1htn, 1hyt, 1iba, 1ido, 1iow, 1iyu, 1kcw, 1kpf, 1lam, 1lay, 1lbu, 1lgr, 1lml, 1lox, 1mfs, 1mla, 1mrp, 1mup, 1nif, 1opc, 1pda, 1pdc, 1pfo, 1phd, 1phm, 1pii, 1pkp, 1poa, 1poc, 1rfs, 1rie, 1rkd, 1rlw, 1skf, 1snc, 1sra, 1thx, 1uch, 1uox, 1ush, 1whi, 1wod, 1xbd, 1xpa, 1ytw, 2abk, 2adr, 2af8, 2cba, 2cmd, 2dkb, 2dri, 2fha, 2fua, 2liv, 2mcm, 2mnr, 2rn2, 2sas, 2vil, 3dfr, 3dni, 3ebx, 3gcb, 3pte, 3ssi, 3tgl, 4enl, 4icb, 4pah, 5eat and 7rsa.

Publication Year: 2005


Efficient identification of critical residues based only on protein structure by network analysis.

(2007) PLoS One 2

PubMed: 17502913 | PubMedCentral: PMC1855080 | DOI: 10.1371/journal.pone.0000421

The 128 PDB names used in this set are: 1a3c, 1a6q, 1a7j, 1aac, 1ac5, 1ah7, 1ak1, 1ako, 1amj, 1an8, 1apq, 1arv, 1atg, 1auz, 1ayl, 1ayx, 1az9, 1b64, 1bag, 1bdb, 1bea, 1bfd, 1bia, 1bif, 1bix, 1bk0, 1bli... 1bn5, 1bor, 1boy, 1bp1, 1bqk, 1brt, 1btl, 1c25, 1ca1, 1cby, 1cex, 1cfb, 1chc, 1chd, 1csh, 1ctn, 1ctt, 1cvl, 1dmr, 1drw, 1dxy, 1ecl, 1eh2, 1emn, 1esl, 1eut, 1far, 1fnc, 1gca, 1htn, 1hyt, 1iba, 1ido, 1iow, 1iyu, 1kcw, 1kpf, 1lam, 1lay, 1lbu, 1lgr, 1lml, 1lox, 1mfs, 1mla, 1mrp, 1mup, 1nif, 1opc, 1pda, 1pdc, 1pfo, 1phd, 1phm, 1pii, 1pkp, 1poa, 1poc, 1rfs, 1rie, 1rkd, 1rlw, 1skf, 1snc, 1sra, 1thx, 1uch, 1uox, 1ush, 1whi, 1wod, 1xbd, 1xpa, 1ytw, 2abk, 2adr, 2af8, 2cba, 2cmd, 2dkb, 2dri, 2fha, 2fua, 2liv, 2mcm, 2mnr, 2rn2, 2sas, 2vil, 3dfr, 3dni, 3ebx, 3gcb, 3pte, 3ssi, 3tgl, 4enl, 4icb, 4pah, 5eat and 7rsa.

Publication Year: 2007


Analysis of the impact of solvent on contacts prediction in proteins.

(2009) BMC Struct Biol 9

PubMed: 19368710 | PubMedCentral: PMC2676287 | DOI: 10.1186/1472-6807-9-22

PFAM ID PDB ID a R (Å) N b % id c L d Ran acc e Acc f R g Opt α h X d dry i Opt Xd α j X d wet | opt α k PF00014 6PTI 1.70 151 33 52 0.096 0.346 3.61 1 9.37 1 11.16 PF0... 705 1AF7 2.00 85 20 57 0.081 0.241 2.65 0.5, 4, 10 6.14 2 7.63 PF00062 5LYZ 2.00 22 46 127 0.043 0.078 1.91 0, 0.5 2.68 0 2.68 PF00018 1BU1 2.60 61 28 56 0.088 0.357 4.06 0.5 12.99 0 12.99 PF03900 1PDA 1.76 21 25 74 0.062 0.237 3.82 2 9.18 0.2 9.99 PF00034 1CTJ 1.10 35 17 89 0.061 0.250 4.10 1 9.13 0.1 10.34 PF01568 1DMR 1.82 88 18 113 0.044 0.050 1.14 0.2, 0.5 10.62 2 12.53 PF00127 8PAZ 1.60 31 29 89 0.055 0.102 1.85 2 0.50 1 4.82 PF01814 2MHR 1.30 295 12 49 0.098 0.400 4.08 0.5, 2 8.39 2 13.14 PF00017 1BMB 1.80 59 28 93 0.058 0.212 3.66 0 – 0.5 5.98 1 8.37 PF01320 1AYI 2.00 45 47 86 0.056 0.233 4.15 0.2 16.04 0 16.04 PF08666 1AME 1.65 171 14 66 0.074 0.273 3.69 0 10.25 0 10.25 PF01337 1A19 2.76 30 25 89 0.065 0.178 2.87 0, 0.1 4.55 0.1 4.72 PF00595 2HB2 2.30 56 19 85 0.062 0.233 3.75 0.5 – 2 10.16 1 11.67 PF00531 1WMG 2.10 92 14 82 0.066 0.250 3.79 0 – 0.5 7.67 0.2 7.95 PF00397 1EG3 2.00 73 32 30 0.143 0.467 3.26 2 – 20 6.59 2 8.81 PF01335 2F1S 1.40 40 21 76 0.072 0.237 3.88 0.1, 0.2 5.66 0.2 5.96 PF00619 1CY5 1.30 61 16 85 0.066 0.209 3.43 0.2 – 2 5.09 2 9.42 PF02213 1SYX 2.35 112 28 58 0.083 0.241 2.91 0.5 – 2 7.37 0.5 7.77 PF05743 1UZX 1.85 28 27 118 0.035 0.068 1.98 0.1 7.22 0 7.22 PF00536 1B4F 1.95 69 28 74 0.076 0.395 5.19 0.2 – 2 15.53 2 16.36 PF03114 1ZWW 2.30 29 19 195 0.021 0.074 3.53 0.2 2.41 20 3.99 PF00169 1NTY 1.70 139 10 112 0.050 0.071 1.43 0, 0.2, 0.5 5.46 2 7.53 PF08416 1WVH 1.50 49 28 132 0.040 0.106 2.65 2, 4 0.53 0.1 1.24 PF01981 1WN2 1.20 69 43 116 0.049 0.172 3.52 0.1 – 0.5 7.63 20 12.38 PF03992 1XBW 1.90 116 15 65 0.068 0.125 1.84 0.5 3.34 0 3.34 PF00907 1H6F 1.70 23 49 183 0.032 0.033 1.03 0 – 20 3.30 2 6.03 PF02237 1WPY 1.60 47 21 48 0.094 0.167 1.77 0.5 – 2 -2.83 0.5 0.22 PF08031 2AXR 1.98 64 34 34 0.135 0.235 1.74 0.1, 0.2 -0.05 2 3.37 PF02861 1K6K 1.80 165 21 51 0.098 0.440 4.49 1, 4, 10, 20 9.55 20 13.21 PF02834 1VGJ 1.94 106 14 85 0.048 0.119 2.48 4 – 20 -0.51 4, 10 3.21 PF01423 1KQ1 1.55 128 23 60 0.079 0.167 2.11 0.2, 0.5 5.78 0.1, 0.2 7.14 PF01472 1AS0 1.80 106 24 78 0.058 0.128 2.21 1 – 20 3.57 2, 4 11.45 PF01909 1NO5 1.80 119 14 91 0.059 0.133 2.26 0.1 – 1 4.97 0.2 6.01 PF09261 1R34 1.95 79 31 78 0.069 0.205 2.97 0.1, 0.2 4.87 0.1 6.64 PF01315 1VLB 1.28 28 19 117 0.041 0.207 5.05 1, 2 7.70 2 10.28 PF04545 1KU3 1.80 128 31 54 0.096 0.370 3.86 0, 0.1, 1, 10, 20 12.37 10, 20 12.76 PF00984 1MV8 1.55 24 17 98 0.048 0.184 3.83 0.5 – 20 8.27 0.2 9.78 PF01658 1U1I 1.90 20 31 105 0.049 0.096 1.96 0.1 – 20 1.93 0.5 6.28 PF00745 1GPJ 1.95 34 23 99 0.048 0.100 2.08 0.1 – 0.5 3.17 0.1 4.17 PF03099 1WNL 1.60 65 14 117 0.043 0.121 2.81 0 13.7 0.2 14.20 PF01985 1JO0 1.37 50 23 84 0.064 0.167 2.60 0 – 0.2 6.96 0 6.96 PF08436 1Q0Q 1.90 77 57 94 0.049 0.213 4.34 0 – 0.1 6.91 10 10.15 PF02881 1JPN 1.90 52 19 85 0.063 0.119 1.89 0 – 20 3.94 2 5.78 PF01966 1YNB 1.76 158 12 91 0.057 0.333 5.85 0 – 0.2 -0.79 2 2.20 PF00191 1YII 1.42 178 28 66 0.076 0.273 3.59 0 – 0.2 -0.35 10 1.05 PF00317 1XJE 1.90 79 23 90 0.056 0.178 3.17 0.5 – 2 10.01 0.5 13.16 PF00046 1PUF 1.90 184 37 60 0.082 0.333 4.07 1, 2 6.07 2 8.60 PF00077 5FIV 1.90 48 27 108 0.049 0.093 1.89 2 -1.37 1 3.63 PF00042 1ECN 1.40 73 18 101 0.046 0.163 3.56 1, 2 6.89 2 7.19 a PDB ID; b Number of sequences; c Average sequences pairwise similarity (%); d Reference sequence length; e Random accuracy; f Accuracy for optimal α ; g Improvement ratio over random prediction for optimal α ; h Values for α = 0; i α corresponding to the highest accuracy; j α corresponding to the highest X d ; k X d highest value.

Publication Year: 2009


Generalized spring tensor models for protein fluctuation dynamics and conformation changes.

(2010) BMC Struct Biol 10 Suppl 1

PubMed: 20487510 | PubMedCentral: PMC2873826 | DOI: 10.1186/1472-6807-10-S1-S3

Table 1 The correlation coefficients between the experimental and calculated B-factors using different models Protein R(Å) ANM GNM STeM Protein R(Å) ANM GNM STeM Protein R(Å) A... M GNM STeM 1AAC 1.31 0.7 0.71 0.76 1ADS 1.65 0.77 0.74 0.71 1AHC 2.00 0.79 0.68 0.61 1AKY 1.63 0.56 0.72 0.6 1AMM 1.20 0.56 0.72 0.55 1AMP 1.80 0.62 0.59 0.68 1ARB 1.20 0.78 0.76 0.83 1ARS 1.80 0.14 0.43 0.41 1ARU 1.60 0.7 0.78 0.79 1BKF 1.60 0.52 0.43 0.5 1BPI 1.09 0.43 0.56 0.57 1CDG 2.00 0.65 0.62 0.71 1CEM 1.65 0.51 0.63 0.76 1CNR 1.05 0.34 0.64 0.42 1CNV 1.65 0.69 0.62 0.68 1CPN 1.80 0.51 0.54 0.56 1CSH 1.65 0.44 0.41 0.57 1CTJ 1.10 0.47 0.39 0.62 1CUS 1.25 0.74 0.66 0.76 1DAD 1.60 0.28 0.5 0.42 1DDT 2.00 0.21 -0.01 0.49 1EDE 1.90 0.67 0.63 0.75 1EZM 1.50 0.56 0.6 0.58 1FNC 2.00 0.29 0.59 0.61 1FRD 1.70 0.54 0.83 0.77 1FUS 1.30 0.4 0.63 0.61 1FXD 1.70 0.58 0.56 0.7 1GIA 2.00 0.68 0.67 0.69 1GKY 2.00 0.36 0.55 0.44 1GOF 1.70 0.75 0.76 0.78 1GPR 1.90 0.65 0.62 0.66 1HFC 1.50 0.63 0.38 0.35 1IAB 1.79 0.36 0.42 0.53 1IAG 2.00 0.34 0.52 0.44 1IFC 1.19 0.61 0.67 0.53 1IGD 1.10 0.18 0.44 0.27 1IRO 1.10 0.82 0.51 0.85 1JBC 1.15 0.72 0.7 0.73 1KNB 1.70 0.63 0.66 0.54 1LAM 1.60 0.53 0.63 0.71 1LCT 2.00 0.52 0.57 0.61 1LIS 1.90 0.16 0.43 0.3 1LIT 1.55 0.65 0.62 0.76 1LST 1.80 0.39 0.72 0.73 1MJC 2.00 0.67 0.67 0.61 1MLA 1.50 0.59 0.57 0.54 1MRJ 1.60 0.66 0.49 0.5 1NAR 1.80 0.62 0.76 0.74 1NFP 1.60 0.23 0.48 0.41 1NIF 1.70 0.42 0.58 0.61 1NPK 1.80 0.53 0.55 0.64 1OMP 1.80 0.61 0.63 0.65 1ONC 1.70 0.55 0.7 0.58 1OSA 1.68 0.36 0.42 0.55 1OYC 2.00 0.78 0.73 0.77 1PBE 1.90 0.53 0.61 0.63 1PDA 1.76 0.6 0.76 0.58 1PHB 1.60 0.56 0.52 0.59 1PHP 1.65 0.59 0.63 0.65 1PII 2.00 0.19 0.44 0.28 1PLC 1.33 0.41 0.47 0.42 1POA 1.50 0.54 0.66 0.42 1POC 2.00 0.46 0.52 0.39 1PPN 1.60 0.61 0.64 0.67 1PTF 1.60 0.47 0.6 0.54 1PTX 1.30 0.65 0.51 0.62 1RA9 2.00 0.48 0.61 0.53 1RCF 1.40 0.59 0.63 0.58 1REC 1.90 0.34 0.5 0.49 1RIE 1.50 0.71 0.25 0.52 1RIS 2.00 0.25 0.24 0.47 1RRO 1.30 0.08 0.31 0.36 1SBP 1.70 0.69 0.72 0.67 1SMD 1.60 0.5 0.62 0.67 1SNC 1.65 0.68 0.71 0.72 1THG 1.80 0.5 0.53 0.5 1TML 1.80 0.64 0.64 0.58 1UBI 1.80 0.56 0.69 0.61 1WHI 1.50 0.12 0.33 0.38 1XIC 1.60 0.29 0.4 0.47 2AYH 1.60 0.63 0.73 0.82 2CBA 1.54 0.67 0.75 0.8 2CMD 1.87 0.68 0.6 0.62 2CPL 1.63 0.61 0.6 0.72 2CTC 1.40 0.63 0.67 0.75 2CY3 1.70 0.51 0.5 0.67 2END 1.45 0.63 0.71 0.68 2ERL 1.00 0.74 0.73 0.85 2HFT 1.69 0.63 0.79 0.72 2IHL 1.40 0.62 0.69 0.72 2MCM 1.50 0.78 0.83 0.79 2MHR 1.30 0.65 0.52 0.64 2MNR 1.90 0.46 0.5 0.47 2PHY 1.40 0.54 0.55 0.68 2RAN 1.89 0.43 0.4 0.31 2RHE 1.60 0.28 0.38 0.33 2RN2 1.48 0.68 0.71 0.75 2SIL 1.60 0.43 0.5 0.51 2TGI 1.80 0.69 0.71 0.73 3CHY 1.66 0.61 0.75 0.68 3COX 1.80 0.71 0.71 0.72 3EBX 1.40 0.22 0.58 0.4 3GRS 1.54 0.44 0.57 0.59 3LZM 1.70 0.6 0.52 0.66 3PTE 1.60 0.68 0.83 0.77 4FGF 1.60 0.41 0.27 0.43 4GCR 1.47 0.73 0.81 0.75 4MT2 2.00 0.42 0.37 0.46 5P21 1.35 0.4 0.51 0.45 7RSA 1.26 0.42 0.63 0.59 8ABP 1.49 0.61 0.82 0.62 Column R(Å) gives the resolution of each structure.

Publication Year: 2010


Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Bacillus megaterium.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69

PubMed: 23908040 | PubMedCentral: PMC3729171 | DOI: 10.1107/S1744309113018526

Structure analysis by use of the molecular-replacement program MOLREP (Vagin & Teplyakov, 2010 ▶ ) with E. coli PBGD (47% identity; PDB entry 1pda ; Louie et al. , 1992 ▶ ) as ... he search model was successful and refinement of the B. megaterium PBGD structure is currently in progress using this high-resolution data set.

The X-ray structure of the Arabidopsis thaliana enzyme has recently been solved (PDB entry 4htg ; Roberts et al. , 2013 ▶ ); prior to this, structures were available for Escherichia coli PBGD [PDB entries 1pda (Louie et al. , 1992 ▶ , 1996 ▶ ), 1gtk (Helliwell et al. , 2003 ▶ ), 1ah5 (Hädener et al. , 1999 ▶ ), 1ypn (Helliwell et al. , 1998 ▶ ) and 2ypn (Nieh et al. , 1999 ▶ )] and the human enzyme (PDB entries 3eq1 and 3ecr ; Gill et al. , 2009 ▶ ; Song et al. , 2009 ▶ ).

Publication Year: 2013


Structural insights into E. coli porphobilinogen deaminase during synthesis and exit of 1-hydroxymethylbilane.

(2014) PLoS Comput Biol 10

PubMed: 24603363 | PubMedCentral: PMC3945110 | DOI: 10.1371/journal.pcbi.1003484

Five crystal structures of E. coli PBGD ( EcPBGD): 1GTK [9] , 1YPN [10] , 2YPN [11] , 1AH5 [12] , 1PDA [8] ; two of hPBGD: 3ECR [13] , 3EQ1 [5] ; and most recently, one of Arabidopsis thaliana PBGD (A... PBGD): 4HTG [14] are available in the protein data bank (PDB) [15] .

Publication Year: 2014


Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution.

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 24598743 | PubMedCentral: PMC3949521 | DOI: 10.1107/S139900471303294X

Structure analysis was successful for the crystal 1 data set using the molecular-replacement program MOLREP (Vagin & Teplyakov, 2010 ▶ ) with E. coli PBGD (48% identity; PDB entry 1pda... ; Louie et al. , 1992 ▶ ) as the search model.

Publication Year: 2014